diff --git a/client/gulpfile.js b/client/gulpfile.js
index 5707830e2f23..f0393e438b1e 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -15,7 +15,6 @@ const xml2js = require("xml2js");
 const STATIC_PLUGIN_BUILD_IDS = [
     "annotate_image",
     "chiraviz",
-    "cytoscape",
     "drawrna",
     "editor",
     "example",
@@ -28,7 +27,6 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "mvpapp",
     "nora",
     "nvd3/nvd3_bar",
-    "openlayers",
     "openseadragon",
     "PCA_3Dplot",
     "phylocanvas",
@@ -36,9 +34,8 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "scatterplot",
     "tiffviewer",
     "ts_visjs",
-    "venn",
 ];
-const INSTALL_PLUGIN_BUILD_IDS = ["ngl", "msa"]; // todo: derive from XML
+const INSTALL_PLUGIN_BUILD_IDS = ["cytoscape", "ngl", "msa", "openlayers", "venn", "vizarr"]; // todo: derive from XML
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
 
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index a2521374c650..779417815453 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -11963,6 +11963,21 @@ export interface components {
              */
             workflow_step_id: number;
         };
+        /** InvocationFailureWorkflowParameterInvalidResponse */
+        InvocationFailureWorkflowParameterInvalidResponse: {
+            /**
+             * Details
+             * @description Message raised by validator
+             */
+            details: string;
+            /**
+             * @description discriminator enum property added by openapi-typescript
+             * @enum {string}
+             */
+            reason: "workflow_parameter_invalid";
+            /** Workflow parameter step that failed validation */
+            workflow_step_id: number;
+        };
         /** InvocationInput */
         InvocationInput: {
             /**
@@ -12044,7 +12059,8 @@ export interface components {
             | components["schemas"]["InvocationFailureExpressionEvaluationFailedResponse"]
             | components["schemas"]["InvocationFailureWhenNotBooleanResponse"]
             | components["schemas"]["InvocationUnexpectedFailureResponse"]
-            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"];
+            | components["schemas"]["InvocationEvaluationWarningWorkflowOutputNotFoundResponse"]
+            | components["schemas"]["InvocationFailureWorkflowParameterInvalidResponse"];
         /** InvocationOutput */
         InvocationOutput: {
             /**
diff --git a/client/src/components/Common/ButtonSpinner.vue b/client/src/components/Common/ButtonSpinner.vue
index e2b8def400c1..f87f34b33991 100644
--- a/client/src/components/Common/ButtonSpinner.vue
+++ b/client/src/components/Common/ButtonSpinner.vue
@@ -11,12 +11,14 @@ interface Props {
     wait?: boolean;
     tooltip?: string;
     disabled?: boolean;
+    size?: string;
 }
 
 withDefaults(defineProps<Props>(), {
     wait: false,
     tooltip: undefined,
     disabled: false,
+    size: "md",
 });
 </script>
 
@@ -25,6 +27,7 @@ withDefaults(defineProps<Props>(), {
         v-if="wait"
         v-b-tooltip.hover.bottom
         disabled
+        :size="size"
         variant="info"
         title="Please Wait..."
         class="d-flex flex-nowrap align-items-center text-nowrap">
@@ -38,6 +41,7 @@ withDefaults(defineProps<Props>(), {
         class="d-flex flex-nowrap align-items-center text-nowrap"
         :title="tooltip"
         :disabled="disabled"
+        :size="size"
         @click="$emit('onClick')">
         <FontAwesomeIcon :icon="faPlay" class="mr-2" />
         {{ title }}
diff --git a/client/src/components/Form/FormElement.vue b/client/src/components/Form/FormElement.vue
index ed81622799e1..aa3507808661 100644
--- a/client/src/components/Form/FormElement.vue
+++ b/client/src/components/Form/FormElement.vue
@@ -27,6 +27,7 @@ import FormSelection from "./Elements/FormSelection.vue";
 import FormTags from "./Elements/FormTags.vue";
 import FormText from "./Elements/FormText.vue";
 import FormUpload from "./Elements/FormUpload.vue";
+import FormElementHelpMarkdown from "./FormElementHelpMarkdown.vue";
 
 interface FormElementProps {
     id?: string;
@@ -35,6 +36,7 @@ interface FormElementProps {
     title?: string;
     refreshOnChange?: boolean;
     help?: string;
+    helpFormat?: string;
     error?: string;
     warning?: string;
     disabled?: boolean;
@@ -63,6 +65,7 @@ const props = withDefaults(defineProps<FormElementProps>(), {
     connectedDisableText: "Add connection to module.",
     connectedEnableIcon: "fa fa-times",
     connectedDisableIcon: "fa fa-arrows-alt-h",
+    helpFormat: "html",
     workflowBuildingMode: false,
 });
 
@@ -337,7 +340,13 @@ function onAlert(value: string | undefined) {
         </div>
 
         <div v-if="showPreview" class="ui-form-preview pt-1 pl-2 mt-1">{{ previewText }}</div>
-        <span v-if="Boolean(helpText)" class="ui-form-info form-text text-muted" v-html="helpText" />
+        <span
+            v-if="Boolean(helpText) && helpFormat != 'markdown'"
+            class="ui-form-info form-text text-muted"
+            v-html="helpText" />
+        <span v-else-if="Boolean(helpText)" class="ui-form-info form-text text-muted"
+            ><FormElementHelpMarkdown :content="helpText"
+        /></span>
     </div>
 </template>
 
diff --git a/client/src/components/Form/FormElementHelpMarkdown.vue b/client/src/components/Form/FormElementHelpMarkdown.vue
new file mode 100644
index 000000000000..e6271c9a2124
--- /dev/null
+++ b/client/src/components/Form/FormElementHelpMarkdown.vue
@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { computed, onMounted, ref } from "vue";
+
+import { markup } from "@/components/ObjectStore/configurationMarkdown";
+import { getAppRoot } from "@/onload/loadConfig";
+
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
+const props = defineProps<{
+    content: string;
+}>();
+
+const markdownHtml = computed(() => markup(props.content ?? "", false));
+
+const helpHtml = ref<HTMLDivElement>();
+
+interface InternalTypeReference {
+    element: HTMLElement;
+    term: string;
+}
+
+const internalHelpReferences = ref<InternalTypeReference[]>([]);
+
+function setupPopovers() {
+    internalHelpReferences.value.length = 0;
+    if (helpHtml.value) {
+        const links = helpHtml.value.getElementsByTagName("a");
+        Array.from(links).forEach((link) => {
+            if (link.href.startsWith("gxhelp://")) {
+                const uri = link.href.substr("gxhelp://".length);
+                internalHelpReferences.value.push({ element: link, term: uri });
+                link.href = `${getAppRoot()}help/terms/${uri}`;
+                link.style.color = "inherit";
+                link.style.textDecorationLine = "underline";
+                link.style.textDecorationStyle = "dashed";
+            }
+        });
+    }
+}
+
+onMounted(setupPopovers);
+</script>
+
+<template>
+    <span>
+        <!-- Disable v-html warning because we allow markdown generated HTML
+            in various places in the Galaxy interface. Raw HTML is not allowed
+            here because admin = false in the call to markup.
+        -->
+        <!-- eslint-disable-next-line vue/no-v-html -->
+        <div ref="helpHtml" v-html="markdownHtml" />
+        <span v-for="(value, i) in internalHelpReferences" :key="i">
+            <HelpPopover :target="value.element" :term="value.term" />
+        </span>
+    </span>
+</template>
diff --git a/client/src/components/Form/FormInputs.vue b/client/src/components/Form/FormInputs.vue
index 1421a4b79ea3..fafe1734b478 100644
--- a/client/src/components/Form/FormInputs.vue
+++ b/client/src/components/Form/FormInputs.vue
@@ -11,6 +11,7 @@
                         v-model="input.test_param.value"
                         :type="input.test_param.type"
                         :help="input.test_param.help"
+                        :help-format="input.test_param.help_format"
                         :refresh-on-change="false"
                         :disabled="sustainConditionals"
                         :attributes="input.test_param"
@@ -51,6 +52,7 @@
                 :error="input.error"
                 :warning="input.warning"
                 :help="input.help"
+                :help-format="input.help_format"
                 :refresh-on-change="input.refresh_on_change"
                 :attributes="input.attributes || input"
                 :collapsed-enable-text="collapsedEnableText"
diff --git a/client/src/components/Grid/GridInvocation.vue b/client/src/components/Grid/GridInvocation.vue
index 847127cfa0b7..65aed67b73f7 100644
--- a/client/src/components/Grid/GridInvocation.vue
+++ b/client/src/components/Grid/GridInvocation.vue
@@ -109,7 +109,7 @@ function refreshTable() {
             :extra-props="extraProps"
             :embedded="forStoredWorkflow || forHistory || forBatch">
             <template v-slot:expanded="{ rowData }">
-                <span class="position-absolute ml-4" :data-invocation-id="rowData.id">
+                <span class="mb-2" :data-invocation-id="rowData.id">
                     <small>
                         <b>Last updated: <UtcDate :date="rowData.update_time" mode="elapsed" />; Invocation ID:</b>
                     </small>
diff --git a/client/src/components/Help/HelpPopover.vue b/client/src/components/Help/HelpPopover.vue
index 11ded1f423de..200f76706a2b 100644
--- a/client/src/components/Help/HelpPopover.vue
+++ b/client/src/components/Help/HelpPopover.vue
@@ -12,7 +12,7 @@ defineProps<Props>();
 </script>
 
 <template>
-    <BPopover :target="target" triggers="hover" placement="bottom">
+    <BPopover v-if="target" :target="target" triggers="hover" placement="bottom">
         <HelpTerm :term="term" />
     </BPopover>
 </template>
diff --git a/client/src/components/Help/terms.yml b/client/src/components/Help/terms.yml
index 0ca9bd36bc72..536d08f3dee1 100644
--- a/client/src/components/Help/terms.yml
+++ b/client/src/components/Help/terms.yml
@@ -27,7 +27,12 @@ unix:
     debug what is wrong with the execution of an application.
 
     More information on stack traces can be found on [Wikipedia](https://en.wikipedia.org/wiki/Stack_trace).
+programming:
+  python:
+    regex: |
+      Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in [this Python for Biologists tutorial](https://pythonforbiologists.com/tutorial/regex.html).
 
+      The website [regex101](https://regex101.com/) is a useful playground to explore regular expressions (be sure to enable "Python" as your flavor) and language models such as ChatGPT can help interactively build up and explain regular expressions from natural language prompts or examples.
 galaxy:
   collections:
     flatList: |
diff --git a/client/src/components/History/SwitchToHistoryLink.vue b/client/src/components/History/SwitchToHistoryLink.vue
index 047e9ec93fb3..13916b4e9f3f 100644
--- a/client/src/components/History/SwitchToHistoryLink.vue
+++ b/client/src/components/History/SwitchToHistoryLink.vue
@@ -86,7 +86,7 @@ function viewHistoryInNewTab(history: HistorySummary) {
 <template>
     <div>
         <LoadingSpan v-if="!history" />
-        <div v-else class="history-link">
+        <div v-else class="history-link" data-description="switch to history link">
             <BLink
                 v-b-tooltip.hover.top.noninteractive.html
                 data-description="switch to history link"
diff --git a/client/src/components/JobMetrics/JobMetrics.test.js b/client/src/components/JobMetrics/JobMetrics.test.js
index b8e934489e9d..529bf66a7663 100644
--- a/client/src/components/JobMetrics/JobMetrics.test.js
+++ b/client/src/components/JobMetrics/JobMetrics.test.js
@@ -6,6 +6,8 @@ import { getLocalVue } from "tests/jest/helpers";
 
 import JobMetrics from "./JobMetrics";
 
+const NO_METRICS_MESSAGE = "No metrics available for this job.";
+
 // Ignore all axios calls, data is mocked locally -- just say "OKAY!"
 jest.mock("axios", () => ({
     get: async () => {
@@ -26,7 +28,8 @@ describe("JobMetrics/JobMetrics.vue", () => {
         });
 
         await wrapper.vm.$nextTick();
-        expect(wrapper.find("div").exists()).toBe(false);
+        const alert = wrapper.find(".alert-info");
+        expect(alert.text()).toBe(NO_METRICS_MESSAGE);
     });
 
     it("should group plugins by type", async () => {
diff --git a/client/src/components/JobMetrics/JobMetrics.vue b/client/src/components/JobMetrics/JobMetrics.vue
index 469dc3062e73..78dc294c002c 100644
--- a/client/src/components/JobMetrics/JobMetrics.vue
+++ b/client/src/components/JobMetrics/JobMetrics.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
 import { computed, ref, unref, watch } from "vue";
 
 import { useJobMetricsStore } from "@/stores/jobMetricsStore";
@@ -217,4 +218,5 @@ const estimatedServerInstance = computed(() => {
             :cores-allocated="coresAllocated"
             :memory-allocated-in-mebibyte="memoryAllocatedInMebibyte" />
     </div>
+    <BAlert v-else variant="info" show> No metrics available for this job. </BAlert>
 </template>
diff --git a/client/src/components/RuleBuilder/RegularExpressionInput.vue b/client/src/components/RuleBuilder/RegularExpressionInput.vue
index 3f7c089adf80..b3788e423abe 100644
--- a/client/src/components/RuleBuilder/RegularExpressionInput.vue
+++ b/client/src/components/RuleBuilder/RegularExpressionInput.vue
@@ -1,7 +1,7 @@
 <template>
     <div>
-        <label v-b-tooltip.hover for="regular_expression" :title="title">{{ label }}</label>
-        <span v-b-popover.html="popoverContent" :title="popoverTitle" class="fa fa-question"></span>
+        <label ref="helpTarget" v-b-tooltip.hover for="regular_expression">{{ label }}</label>
+        <HelpPopover :target="$refs.helpTarget" term="programming.python.regex" />
         <input
             v-b-tooltip.hover.left
             :title="title"
@@ -16,7 +16,10 @@
 <script>
 import _l from "utils/localization";
 
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
 export default {
+    components: { HelpPopover },
     props: {
         target: {
             required: true,
@@ -32,11 +35,6 @@ export default {
         popoverTitle() {
             return _l("Regular Expressions");
         },
-        popoverContent() {
-            return _l(
-                `Regular expressions are patterns used to match character combinations in strings. This input accepts Python-style regular expressions, find more information about these in <a href="https://pythonforbiologists.com/tutorial/regex.html">this Python for Biologists tutorial</a>.`
-            );
-        },
     },
 };
 </script>
diff --git a/client/src/components/Workflow/Invocation/InvocationScrollList.vue b/client/src/components/Workflow/Invocation/InvocationScrollList.vue
index f42dd3b858ed..2240a3d8c315 100644
--- a/client/src/components/Workflow/Invocation/InvocationScrollList.vue
+++ b/client/src/components/Workflow/Invocation/InvocationScrollList.vue
@@ -96,12 +96,10 @@ const route = useRoute();
 const router = useRouter();
 
 function cardClicked(invocation: WorkflowInvocation) {
-    let path = `/workflows/invocations/${invocation.id}`;
     if (props.inPanel) {
-        path += "?from_panel=true";
         emit("invocation-clicked");
     }
-    router.push(path);
+    router.push(`/workflows/invocations/${invocation.id}`);
 }
 
 function scrollToTop() {
@@ -204,10 +202,14 @@ function workflowName(workflowId: string) {
                         @click="() => cardClicked(invocation)">
                         <div class="overflow-auto w-100">
                             <Heading bold size="text" icon="fa-sitemap">
-                                <span class="truncate-3-lines">{{ workflowName(invocation.workflow_id) }}</span>
+                                <span class="truncate-n-lines three-lines">
+                                    {{ workflowName(invocation.workflow_id) }}
+                                </span>
                             </Heading>
                             <Heading size="text" icon="fa-hdd">
-                                <small class="text-muted">{{ historyName(invocation.history_id) }}</small>
+                                <small class="text-muted truncate-n-lines two-lines">
+                                    {{ historyName(invocation.history_id) }}
+                                </small>
                             </Heading>
                             <div class="d-flex justify-content-between">
                                 <BBadge v-b-tooltip.noninteractive.hover pill>
@@ -257,12 +259,19 @@ function workflowName(workflowId: string) {
 </template>
 
 <style scoped lang="scss">
-@import "theme/blue.scss";
-
-.truncate-3-lines {
+.truncate-n-lines {
     display: -webkit-box;
-    -webkit-line-clamp: 3;
     -webkit-box-orient: vertical;
     overflow: hidden;
+    word-break: break-word;
+    overflow-wrap: break-word;
+    &.three-lines {
+        -webkit-line-clamp: 3;
+        line-clamp: 3;
+    }
+    &.two-lines {
+        -webkit-line-clamp: 2;
+        line-clamp: 2;
+    }
 }
 </style>
diff --git a/client/src/components/Workflow/List/WorkflowIndicators.vue b/client/src/components/Workflow/List/WorkflowIndicators.vue
index 92ccac96c4ae..10f841277c80 100644
--- a/client/src/components/Workflow/List/WorkflowIndicators.vue
+++ b/client/src/components/Workflow/List/WorkflowIndicators.vue
@@ -17,6 +17,7 @@ library.add(faFileImport, faGlobe, faShieldAlt, faUsers, faUser);
 interface Props {
     workflow: any;
     publishedView: boolean;
+    noEditTime?: boolean;
 }
 
 const props = defineProps<Props>();
@@ -118,7 +119,7 @@ function onViewUserPublished() {
             <FontAwesomeIcon :icon="faFileImport" fixed-width @click="onCopyLink" />
         </BButton>
 
-        <span class="mr-1">
+        <span v-if="!noEditTime" class="mr-1">
             <small>
                 edited
                 <UtcDate :date="workflow.update_time" mode="elapsed" />
@@ -136,8 +137,9 @@ function onViewUserPublished() {
         </BBadge>
 
         <BBadge
-            v-if="publishedView"
+            v-if="publishedView && workflow.published"
             v-b-tooltip.noninteractive.hover
+            data-description="published owner badge"
             class="outline-badge cursor-pointer mx-1"
             :title="publishedTitle"
             @click="onViewUserPublished">
diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index 1296010ba689..18a9389654eb 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -199,7 +199,7 @@ defineExpose({
                         Workflow submission failed: {{ submissionError }}
                     </BAlert>
                     <WorkflowRunFormSimple
-                        v-else-if="fromVariant === 'simple'"
+                        v-if="fromVariant === 'simple'"
                         :model="workflowModel"
                         :target-history="simpleFormTargetHistory"
                         :use-job-cache="simpleFormUseJobCache"
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index feb1bb1b2ac2..802ebac376a4 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,56 +1,59 @@
 <template>
     <div>
-        <div v-if="isConfigLoaded" class="h4 clearfix mb-3">
+        <div v-if="isConfigLoaded">
             <BAlert v-if="!canRunOnHistory" variant="warning" show>
                 <span v-localize>
                     The workflow cannot run because the current history is immutable. Please select a different history
                     or send the results to a new one using the run settings ⚙️
                 </span>
             </BAlert>
-            <b>Workflow: {{ model.name }}</b> <i>(version: {{ model.runData.version + 1 }})</i>
-            <ButtonSpinner
-                id="run-workflow"
-                :wait="waitingForRequest"
-                :disabled="hasValidationErrors || !canRunOnHistory"
-                class="float-right"
-                title="Run Workflow"
-                @onClick="onExecute" />
-            <b-dropdown
-                v-if="showRuntimeSettings(currentUser)"
-                id="dropdown-form"
-                ref="dropdown"
-                class="workflow-run-settings float-right"
-                style="margin-right: 10px"
-                title="Workflow Run Settings"
-                no-caret>
-                <template v-slot:button-content>
-                    <span class="fa fa-cog" />
+            <WorkflowNavigationTitle
+                :workflow-id="model.runData.workflow_id"
+                :run-disabled="hasValidationErrors || !canRunOnHistory"
+                :run-waiting="waitingForRequest"
+                @on-execute="onExecute">
+                <template v-slot:workflow-run-actions>
+                    <b-dropdown
+                        v-if="showRuntimeSettings(currentUser)"
+                        id="dropdown-form"
+                        ref="dropdown"
+                        class="workflow-run-settings"
+                        title="Workflow Run Settings"
+                        size="sm"
+                        variant="link"
+                        no-caret>
+                        <template v-slot:button-content>
+                            <span class="fa fa-cog" />
+                        </template>
+                        <b-dropdown-form>
+                            <b-form-checkbox v-model="sendToNewHistory" class="workflow-run-settings-target">
+                                Send results to a new history
+                            </b-form-checkbox>
+                            <b-form-checkbox
+                                v-if="reuseAllowed(currentUser)"
+                                v-model="useCachedJobs"
+                                title="This may skip executing jobs that you have already run.">
+                                Attempt to re-use jobs with identical parameters?
+                            </b-form-checkbox>
+                            <b-form-checkbox
+                                v-if="isConfigLoaded && config.object_store_allows_id_selection"
+                                v-model="splitObjectStore">
+                                Send outputs and intermediate to different storage locations?
+                            </b-form-checkbox>
+                            <WorkflowStorageConfiguration
+                                v-if="isConfigLoaded && config.object_store_allows_id_selection"
+                                :split-object-store="splitObjectStore"
+                                :invocation-preferred-object-store-id="preferredObjectStoreId"
+                                :invocation-intermediate-preferred-object-store-id="preferredIntermediateObjectStoreId"
+                                @updated="onStorageUpdate">
+                            </WorkflowStorageConfiguration>
+                        </b-dropdown-form>
+                    </b-dropdown>
                 </template>
-                <b-dropdown-form>
-                    <b-form-checkbox v-model="sendToNewHistory" class="workflow-run-settings-target">
-                        Send results to a new history
-                    </b-form-checkbox>
-                    <b-form-checkbox
-                        v-if="reuseAllowed(currentUser)"
-                        v-model="useCachedJobs"
-                        title="This may skip executing jobs that you have already run.">
-                        Attempt to re-use jobs with identical parameters?
-                    </b-form-checkbox>
-                    <b-form-checkbox
-                        v-if="isConfigLoaded && config.object_store_allows_id_selection"
-                        v-model="splitObjectStore">
-                        Send outputs and intermediate to different storage locations?
-                    </b-form-checkbox>
-                    <WorkflowStorageConfiguration
-                        v-if="isConfigLoaded && config.object_store_allows_id_selection"
-                        :split-object-store="splitObjectStore"
-                        :invocation-preferred-object-store-id="preferredObjectStoreId"
-                        :invocation-intermediate-preferred-object-store-id="preferredIntermediateObjectStoreId"
-                        @updated="onStorageUpdate">
-                    </WorkflowStorageConfiguration>
-                </b-dropdown-form>
-            </b-dropdown>
+            </WorkflowNavigationTitle>
         </div>
+
+        <WorkflowAnnotation :workflow-id="model.runData.workflow_id" :history-id="model.historyId" show-details />
         <FormDisplay
             :inputs="formInputs"
             :allow-empty-value-on-required-input="true"
@@ -62,7 +65,6 @@
 </template>
 
 <script>
-import ButtonSpinner from "components/Common/ButtonSpinner";
 import FormDisplay from "components/Form/FormDisplay";
 import { allowCachedJobs } from "components/Tool/utilities";
 import { isWorkflowInput } from "components/Workflow/constants";
@@ -76,10 +78,14 @@ import { useUserStore } from "@/stores/userStore";
 import { invokeWorkflow } from "./services";
 import WorkflowStorageConfiguration from "./WorkflowStorageConfiguration";
 
+import WorkflowAnnotation from "../../Workflow/WorkflowAnnotation.vue";
+import WorkflowNavigationTitle from "../WorkflowNavigationTitle.vue";
+
 export default {
     components: {
-        ButtonSpinner,
         FormDisplay,
+        WorkflowAnnotation,
+        WorkflowNavigationTitle,
         WorkflowStorageConfiguration,
     },
     props: {
diff --git a/client/src/components/Workflow/Run/WorkflowRunSuccess.vue b/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
index 13d9d6cb8b55..c51868e53705 100644
--- a/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunSuccess.vue
@@ -33,7 +33,7 @@ const targetHistories = props.invocations.reduce((histories, invocation) => {
 }, [] as string[]);
 const wasNewHistoryTarget =
     props.invocations.length > 0 &&
-    props.invocations[0]?.history_id &&
+    !!props.invocations[0]?.history_id &&
     historyStore.currentHistoryId !== props.invocations[0].history_id;
 </script>
 
@@ -51,7 +51,7 @@ const wasNewHistoryTarget =
         <WorkflowInvocationState
             v-else-if="props.invocations.length === 1 && props.invocations[0]"
             :invocation-id="props.invocations[0].id"
-            :new-history-target="wasNewHistoryTarget ? props.invocations[0].history_id : undefined"
+            :new-history-target="wasNewHistoryTarget"
             is-full-page
             success />
         <div id="webhook-view"></div>
diff --git a/client/src/components/Workflow/WorkflowAnnotation.test.ts b/client/src/components/Workflow/WorkflowAnnotation.test.ts
new file mode 100644
index 000000000000..abb7a4f5c062
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowAnnotation.test.ts
@@ -0,0 +1,168 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
+import { mount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { useServerMock } from "@/api/client/__mocks__";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
+import WorkflowAnnotation from "./WorkflowAnnotation.vue";
+
+// Constants
+const WORKFLOW_OWNER = "test-user";
+const OTHER_USER = "other-user";
+const WORKFLOW_UPDATE_TIME = "2023-01-01T00:00:00.000Z";
+const INVOCATION_TIME = "2024-01-01T00:00:00.000Z";
+const SAMPLE_WORKFLOW = {
+    id: "workflow-id",
+    name: "workflow-name",
+    owner: WORKFLOW_OWNER,
+    version: 1,
+    update_time: WORKFLOW_UPDATE_TIME,
+};
+const OTHER_USER_WORKFLOW_ID = "other-user-workflow-id";
+const SAMPLE_RUN_COUNT = 100;
+const TEST_HISTORY_ID = "test-history-id";
+const TEST_HISTORY = {
+    id: TEST_HISTORY_ID,
+    name: "fake-history-name",
+};
+
+const SELECTORS = {
+    RUN_COUNT: ".workflow-invocations-count",
+    INDICATORS_LINK: '[data-description="published owner badge"]',
+    SWITCH_TO_HISTORY_LINK: "[data-description='switch to history link']",
+    TIME_INFO: '[data-description="workflow annotation time info"]',
+    DATE: '[data-description="workflow annotation date"]',
+};
+
+// Mock the workflow store to return the sample workflow
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((id: string) => {
+                if (id === OTHER_USER_WORKFLOW_ID) {
+                    return { ...SAMPLE_WORKFLOW, id: OTHER_USER_WORKFLOW_ID, published: true };
+                }
+                return SAMPLE_WORKFLOW;
+            }),
+        }),
+    };
+});
+
+jest.mock("@/stores/historyStore"),
+    () => {
+        const originalModule = jest.requireActual("@/stores/historyStore");
+        return {
+            ...originalModule,
+            useHistoryStore: () => ({
+                ...originalModule.useHistoryStore(),
+                getHistoryById: jest.fn().mockImplementation(() => TEST_HISTORY),
+            }),
+        };
+    };
+
+const localVue = getLocalVue();
+const { server, http } = useServerMock();
+
+/**
+ * Mounts the WorkflowAnnotation component with props/stores adjusted given the parameters
+ * @param version The version of the component to mount (`run_form` or `invocation` view)
+ * @param ownsWorkflow Whether the user owns the workflow
+ * @returns The wrapper object
+ */
+async function mountWorkflowAnnotation(version: "run_form" | "invocation", ownsWorkflow = true) {
+    server.use(
+        http.get("/api/histories/{history_id}", ({ response }) => {
+            return response(200).json(TEST_HISTORY);
+        })
+    );
+    server.use(
+        http.get("/api/workflows/{workflow_id}/counts", ({ response }) => {
+            return response(200).json({ scheduled: SAMPLE_RUN_COUNT });
+        })
+    );
+
+    const wrapper = mount(WorkflowAnnotation as object, {
+        propsData: {
+            workflowId: ownsWorkflow ? SAMPLE_WORKFLOW.id : OTHER_USER_WORKFLOW_ID,
+            historyId: TEST_HISTORY_ID,
+            invocationUpdateTime: version === "invocation" ? INVOCATION_TIME : undefined,
+            showDetails: version === "run_form",
+        },
+        localVue,
+        pinia: createTestingPinia(),
+        stubs: {
+            FontAwesomeIcon: true,
+        },
+    });
+
+    const historyStore = useHistoryStore();
+    historyStore.setCurrentHistoryId(TEST_HISTORY_ID);
+
+    const userStore = useUserStore();
+    userStore.currentUser = getFakeRegisteredUser({
+        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
+    });
+
+    await flushPromises();
+
+    return { wrapper };
+}
+
+describe("WorkflowAnnotation renders", () => {
+    it("(always) the run count and history, not indicators if owned not published", async () => {
+        async function checkHasRunCount(version: "run_form" | "invocation") {
+            const { wrapper } = await mountWorkflowAnnotation(version);
+
+            const runCount = wrapper.find(SELECTORS.RUN_COUNT);
+            expect(runCount.text()).toContain("workflow runs:");
+            expect(runCount.text()).toContain(SAMPLE_RUN_COUNT.toString());
+
+            expect(wrapper.find(SELECTORS.SWITCH_TO_HISTORY_LINK).text()).toBe(TEST_HISTORY.name);
+
+            // Since this is the user's own workflow, the indicators link
+            // (to view all published workflows by the owner) should not be present
+            expect(wrapper.find(SELECTORS.INDICATORS_LINK).exists()).toBe(false);
+        }
+        await checkHasRunCount("run_form");
+        await checkHasRunCount("invocation");
+    });
+
+    it("workflow indicators if the user does not own the workflow", async () => {
+        // we assume it is another user's published workflow in this case
+
+        async function checkHasIndicators(version: "run_form" | "invocation") {
+            const { wrapper } = await mountWorkflowAnnotation(version, false);
+
+            const indicatorsLink = wrapper.find(SELECTORS.INDICATORS_LINK);
+            expect(indicatorsLink.text()).toBe(WORKFLOW_OWNER);
+            expect(indicatorsLink.attributes("title")).toContain(
+                `Click to view all published workflows by '${WORKFLOW_OWNER}'`
+            );
+        }
+        await checkHasIndicators("run_form");
+        await checkHasIndicators("invocation");
+    });
+
+    it("renders time since edit if run form view", async () => {
+        const { wrapper } = await mountWorkflowAnnotation("run_form");
+
+        const timeInfo = wrapper.find(SELECTORS.TIME_INFO);
+        expect(timeInfo.text()).toContain("edited");
+        expect(timeInfo.find(SELECTORS.DATE).attributes("title")).toBe(WORKFLOW_UPDATE_TIME);
+    });
+
+    it("renders time since invocation if invocation view", async () => {
+        const { wrapper } = await mountWorkflowAnnotation("invocation");
+
+        const timeInfo = wrapper.find(SELECTORS.TIME_INFO);
+        expect(timeInfo.text()).toContain("invoked");
+        expect(timeInfo.find(SELECTORS.DATE).attributes("title")).toBe(INVOCATION_TIME);
+    });
+});
diff --git a/client/src/components/Workflow/WorkflowAnnotation.vue b/client/src/components/Workflow/WorkflowAnnotation.vue
new file mode 100644
index 000000000000..28559a7313d8
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowAnnotation.vue
@@ -0,0 +1,99 @@
+<script setup lang="ts">
+import { faClock } from "@fortawesome/free-regular-svg-icons";
+import { faExclamation, faHdd } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BBadge } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed } from "vue";
+
+import { isRegisteredUser } from "@/api";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
+import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
+
+import TextSummary from "../Common/TextSummary.vue";
+import SwitchToHistoryLink from "../History/SwitchToHistoryLink.vue";
+import StatelessTags from "../TagsMultiselect/StatelessTags.vue";
+import UtcDate from "../UtcDate.vue";
+import WorkflowInvocationsCount from "../Workflow/WorkflowInvocationsCount.vue";
+import WorkflowIndicators from "@/components/Workflow/List/WorkflowIndicators.vue";
+
+interface Props {
+    workflowId: string;
+    invocationUpdateTime?: string;
+    historyId: string;
+    showDetails?: boolean;
+    newHistoryTarget?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    invocationUpdateTime: undefined,
+});
+
+const { workflow } = useWorkflowInstance(props.workflowId);
+
+const { currentUser } = storeToRefs(useUserStore());
+const owned = computed(() => {
+    if (isRegisteredUser(currentUser.value) && workflow.value) {
+        return currentUser.value.username === workflow.value.owner;
+    } else {
+        return false;
+    }
+});
+
+const description = computed(() => {
+    if (workflow.value?.annotation) {
+        return workflow.value.annotation?.trim();
+    } else {
+        return null;
+    }
+});
+
+const timeElapsed = computed(() => {
+    return props.invocationUpdateTime || workflow.value?.update_time;
+});
+
+const workflowTags = computed(() => {
+    return workflow.value?.tags || [];
+});
+</script>
+
+<template>
+    <div v-if="workflow" class="pb-2 pl-2">
+        <div class="d-flex justify-content-between align-items-center">
+            <div>
+                <i v-if="timeElapsed" data-description="workflow annotation time info">
+                    <FontAwesomeIcon :icon="faClock" class="mr-1" />
+                    <span v-localize>
+                        {{ props.invocationUpdateTime ? "invoked" : "edited" }}
+                    </span>
+                    <UtcDate :date="timeElapsed" mode="elapsed" data-description="workflow annotation date" />
+                </i>
+                <span class="d-flex flex-gapx-1 align-items-center">
+                    <FontAwesomeIcon :icon="faHdd" />Input History:
+                    <SwitchToHistoryLink :history-id="props.historyId" />
+                    <BBadge
+                        v-if="props.newHistoryTarget && useHistoryStore().currentHistoryId !== props.historyId"
+                        v-b-tooltip.hover.noninteractive
+                        data-description="new history badge"
+                        role="button"
+                        variant="info"
+                        title="Results generated in a new history. Click on history name to switch to that history.">
+                        <FontAwesomeIcon :icon="faExclamation" />
+                    </BBadge>
+                </span>
+            </div>
+            <slot name="middle-content" />
+            <div class="d-flex align-items-center">
+                <div class="d-flex flex-column align-items-end mr-2">
+                    <WorkflowIndicators :workflow="workflow" published-view no-edit-time />
+                    <WorkflowInvocationsCount v-if="owned" class="mr-1" :workflow="workflow" />
+                </div>
+            </div>
+        </div>
+        <div v-if="props.showDetails">
+            <TextSummary v-if="description" class="my-1" :description="description" />
+            <StatelessTags v-if="workflowTags.length" :value="workflowTags" :disabled="true" />
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Workflow/WorkflowNavigationTitle.test.ts b/client/src/components/Workflow/WorkflowNavigationTitle.test.ts
new file mode 100644
index 000000000000..75dfa51431a9
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowNavigationTitle.test.ts
@@ -0,0 +1,199 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getFakeRegisteredUser } from "@tests/test-data";
+import { shallowMount } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { getLocalVue } from "tests/jest/helpers";
+
+import sampleInvocation from "@/components/Workflow/test/json/invocation.json";
+import { useUserStore } from "@/stores/userStore";
+
+import WorkflowNavigationTitle from "./WorkflowNavigationTitle.vue";
+
+// Constants
+const WORKFLOW_OWNER = "test-user";
+const OTHER_USER = "other-user";
+const UNIMPORTABLE_WORKFLOW_ID = "invalid-workflow-id";
+const UNIMPORTABLE_WORKFLOW_INSTANCE_ID = "invalid-instance-id";
+const SAMPLE_WORKFLOW = {
+    id: "workflow-id",
+    name: "workflow-name",
+    owner: WORKFLOW_OWNER,
+    version: 1,
+};
+const IMPORT_ERROR_MESSAGE = "Failed to import workflow";
+
+const SELECTORS = {
+    WORKFLOW_HEADING: "[data-description='workflow heading']",
+    ACTIONS_BUTTON_GROUP: "bbuttongroup-stub",
+    EDIT_WORKFLOW_BUTTON: `bbutton-stub[title='<b>Edit</b><br>${SAMPLE_WORKFLOW.name}']`,
+    IMPORT_WORKFLOW_BUTTON: "[data-description='import workflow button']",
+    EXECUTE_WORKFLOW_BUTTON: "[data-description='execute workflow button']",
+    ROUTE_TO_RUN_BUTTON: "[data-description='route to workflow run button']",
+    ALERT_MESSAGE: "balert-stub",
+};
+
+// Mock the copyWorkflow function for importing a workflow
+jest.mock("components/Workflow/workflows.services", () => ({
+    copyWorkflow: jest.fn().mockImplementation((workflowId: string) => {
+        if (workflowId === UNIMPORTABLE_WORKFLOW_ID) {
+            throw new Error(IMPORT_ERROR_MESSAGE);
+        }
+        return SAMPLE_WORKFLOW;
+    }),
+}));
+
+// Mock the workflow store to return the sample workflow
+jest.mock("@/stores/workflowStore", () => {
+    const originalModule = jest.requireActual("@/stores/workflowStore");
+    return {
+        ...originalModule,
+        useWorkflowStore: () => ({
+            ...originalModule.useWorkflowStore(),
+            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((instanceId: string) => {
+                if (instanceId === UNIMPORTABLE_WORKFLOW_INSTANCE_ID) {
+                    return { ...SAMPLE_WORKFLOW, id: UNIMPORTABLE_WORKFLOW_ID };
+                }
+                return SAMPLE_WORKFLOW;
+            }),
+        }),
+    };
+});
+
+const localVue = getLocalVue();
+
+/**
+ * Mounts the WorkflowNavigationTitle component with props/stores adjusted given the parameters
+ * @param version The version of the component to mount (`run_form` or `invocation` view)
+ * @param ownsWorkflow Whether the user owns the workflow associated with the invocation
+ * @param unimportableWorkflow Whether the workflow import should fail
+ * @returns The wrapper object, and the mockRouter object
+ */
+async function mountWorkflowNavigationTitle(
+    version: "run_form" | "invocation",
+    ownsWorkflow = true,
+    unimportableWorkflow = false
+) {
+    const mockRouter = {
+        push: jest.fn(),
+    };
+
+    let workflowId: string;
+    let invocation;
+    if (version === "invocation") {
+        workflowId = !unimportableWorkflow ? sampleInvocation.workflow_id : UNIMPORTABLE_WORKFLOW_INSTANCE_ID;
+        invocation = {
+            ...sampleInvocation,
+            workflow_id: workflowId,
+        };
+    } else {
+        workflowId = !unimportableWorkflow ? SAMPLE_WORKFLOW.id : UNIMPORTABLE_WORKFLOW_INSTANCE_ID;
+        invocation = undefined;
+    }
+
+    const wrapper = shallowMount(WorkflowNavigationTitle as object, {
+        propsData: {
+            invocation,
+            workflowId,
+        },
+        localVue,
+        mocks: {
+            $router: mockRouter,
+        },
+        pinia: createTestingPinia(),
+    });
+
+    const userStore = useUserStore();
+    userStore.currentUser = getFakeRegisteredUser({
+        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
+    });
+
+    return { wrapper, mockRouter };
+}
+
+describe("WorkflowNavigationTitle renders", () => {
+    it("the workflow name in header and run button in actions; invocation version", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation");
+
+        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
+        expect(heading.text()).toContain(`Invoked Workflow: ${SAMPLE_WORKFLOW.name}`);
+        expect(heading.text()).toContain(`(version: ${SAMPLE_WORKFLOW.version + 1})`);
+
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const runButton = actionsGroup.find(SELECTORS.ROUTE_TO_RUN_BUTTON);
+        expect(runButton.attributes("title")).toContain("Rerun");
+        expect(runButton.attributes("title")).toContain(SAMPLE_WORKFLOW.name);
+    });
+
+    it("the workflow name in header and run button in actions; run form version", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("run_form");
+
+        const heading = wrapper.find(SELECTORS.WORKFLOW_HEADING);
+        expect(heading.text()).toContain(`Workflow: ${SAMPLE_WORKFLOW.name}`);
+        expect(heading.text()).toContain(`(version: ${SAMPLE_WORKFLOW.version + 1})`);
+
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const runButton = actionsGroup.find(SELECTORS.EXECUTE_WORKFLOW_BUTTON);
+        expect(runButton.attributes("title")).toContain("Run");
+    });
+
+    it("edit button if user owns the workflow", async () => {
+        async function findAndClickEditButton(version: "invocation" | "run_form") {
+            const { wrapper, mockRouter } = await mountWorkflowNavigationTitle(version);
+            const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+
+            const editButton = actionsGroup.find(SELECTORS.EDIT_WORKFLOW_BUTTON);
+            await editButton.trigger("click");
+            await flushPromises();
+
+            expect(mockRouter.push).toHaveBeenCalledTimes(1);
+            expect(mockRouter.push).toHaveBeenCalledWith(
+                `/workflows/edit?id=${SAMPLE_WORKFLOW.id}&version=${SAMPLE_WORKFLOW.version}`
+            );
+        }
+        await findAndClickEditButton("invocation");
+        await findAndClickEditButton("run_form");
+    });
+
+    it("import button instead if user does not own the workflow", async () => {
+        async function findImportButton(version: "invocation" | "run_form") {
+            const { wrapper } = await mountWorkflowNavigationTitle(version, false);
+            const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+            const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+            expect(importButton.exists()).toBe(true);
+        }
+        await findImportButton("invocation");
+        await findImportButton("run_form");
+    });
+});
+
+describe("Importing a workflow in WorkflowNavigationTitle", () => {
+    // We only need to test the `invocation` version because the button is the same in both versions
+
+    it("should show a confirmation dialog when the import is successful", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation", false);
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+
+        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
+        await importButton.props().action();
+        await flushPromises();
+
+        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
+        expect(alert.attributes("variant")).toBe("info");
+        expect(alert.text()).toContain(`Workflow ${SAMPLE_WORKFLOW.name} imported successfully`);
+    });
+
+    it("should show an error dialog when the import fails", async () => {
+        const { wrapper } = await mountWorkflowNavigationTitle("invocation", false, true);
+        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
+        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
+
+        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
+        await importButton.props().action();
+        await flushPromises();
+
+        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
+        expect(alert.attributes("variant")).toBe("danger");
+        expect(alert.text()).toContain(IMPORT_ERROR_MESSAGE);
+    });
+});
diff --git a/client/src/components/Workflow/WorkflowNavigationTitle.vue b/client/src/components/Workflow/WorkflowNavigationTitle.vue
new file mode 100644
index 000000000000..4a5b9a413716
--- /dev/null
+++ b/client/src/components/Workflow/WorkflowNavigationTitle.vue
@@ -0,0 +1,168 @@
+<script setup lang="ts">
+import { faEdit, faSitemap, faUpload } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { BAlert, BButton, BButtonGroup } from "bootstrap-vue";
+import { storeToRefs } from "pinia";
+import { computed, ref } from "vue";
+import { RouterLink } from "vue-router";
+import { useRouter } from "vue-router/composables";
+
+import { isRegisteredUser } from "@/api";
+import type { WorkflowInvocationElementView } from "@/api/invocations";
+import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
+import { useUserStore } from "@/stores/userStore";
+import type { Workflow } from "@/stores/workflowStore";
+import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
+
+import { copyWorkflow } from "./workflows.services";
+
+import AsyncButton from "../Common/AsyncButton.vue";
+import ButtonSpinner from "../Common/ButtonSpinner.vue";
+import WorkflowRunButton from "./WorkflowRunButton.vue";
+
+const router = useRouter();
+
+interface Props {
+    invocation?: WorkflowInvocationElementView;
+    workflowId: string;
+    runDisabled?: boolean;
+    runWaiting?: boolean;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+    invocation: undefined,
+});
+
+const emit = defineEmits<{
+    (e: "on-execute"): void;
+}>();
+
+const { workflow, error } = useWorkflowInstance(props.workflowId);
+
+const { currentUser, isAnonymous } = storeToRefs(useUserStore());
+const owned = computed(() => {
+    if (isRegisteredUser(currentUser.value) && workflow.value) {
+        return currentUser.value.username === workflow.value.owner;
+    } else {
+        return false;
+    }
+});
+
+const importErrorMessage = ref<string | null>(null);
+const importedWorkflow = ref<Workflow | null>(null);
+const workflowImportedAttempted = ref(false);
+
+async function onImport() {
+    if (!workflow.value || !workflow.value.owner) {
+        return;
+    }
+    try {
+        const wf = await copyWorkflow(workflow.value.id, workflow.value.owner);
+        importedWorkflow.value = wf as unknown as Workflow;
+    } catch (error) {
+        importErrorMessage.value = errorMessageAsString(error, "Failed to import workflow");
+    } finally {
+        workflowImportedAttempted.value = true;
+    }
+}
+
+function getWorkflowName(): string {
+    return workflow.value?.name || "...";
+}
+
+const workflowImportTitle = computed(() => {
+    if (isAnonymous.value) {
+        return localize("Login to import this workflow");
+    } else if (workflowImportedAttempted.value) {
+        return localize("Workflow imported");
+    } else {
+        return localize("Import this workflow");
+    }
+});
+</script>
+
+<template>
+    <div>
+        <div>
+            <BAlert v-if="importErrorMessage" variant="danger" dismissible show @dismissed="importErrorMessage = null">
+                {{ importErrorMessage }}
+            </BAlert>
+            <BAlert v-else-if="importedWorkflow" variant="info" dismissible show @dismissed="importedWorkflow = null">
+                <span>
+                    Workflow <b>{{ importedWorkflow.name }}</b> imported successfully.
+                </span>
+                <RouterLink to="/workflows/list">Click here</RouterLink> to view the imported workflow in the workflows
+                list.
+            </BAlert>
+
+            <BAlert v-if="error" variant="danger" show>{{ error }}</BAlert>
+
+            <div v-if="workflow" class="ui-portlet-section">
+                <div class="d-flex portlet-header align-items-center">
+                    <div class="flex-grow-1" data-description="workflow heading">
+                        <div class="px-1">
+                            <FontAwesomeIcon :icon="faSitemap" />
+                            <b class="mx-1">
+                                {{ props.invocation ? "Invoked " : "" }}Workflow: {{ getWorkflowName() }}
+                            </b>
+                            <i>(version: {{ workflow.version + 1 }})</i>
+                        </div>
+                    </div>
+                    <BButtonGroup>
+                        <BButton
+                            v-if="owned && workflow"
+                            v-b-tooltip.hover.noninteractive.html
+                            size="sm"
+                            :title="
+                                !workflow.deleted
+                                    ? `<b>Edit</b><br>${getWorkflowName()}`
+                                    : 'This workflow has been deleted.'
+                            "
+                            variant="link"
+                            :disabled="workflow.deleted"
+                            @click="router.push(`/workflows/edit?id=${workflow.id}&version=${workflow.version}`)">
+                            <FontAwesomeIcon :icon="faEdit" fixed-width />
+                        </BButton>
+                        <AsyncButton
+                            v-else
+                            v-b-tooltip.hover.noninteractive
+                            data-description="import workflow button"
+                            size="sm"
+                            :disabled="isAnonymous || workflowImportedAttempted"
+                            :title="workflowImportTitle"
+                            :icon="faUpload"
+                            variant="link"
+                            :action="onImport">
+                        </AsyncButton>
+
+                        <slot name="workflow-run-actions" />
+
+                        <ButtonSpinner
+                            v-if="!props.invocation"
+                            id="run-workflow"
+                            data-description="execute workflow button"
+                            :wait="runWaiting"
+                            :disabled="runDisabled"
+                            size="sm"
+                            title="Run"
+                            @onClick="emit('on-execute')" />
+                        <WorkflowRunButton
+                            v-else
+                            :id="workflow.id"
+                            data-description="route to workflow run button"
+                            variant="link"
+                            :title="
+                                !workflow.deleted
+                                    ? `<b>Rerun</b><br>${getWorkflowName()}`
+                                    : 'This workflow has been deleted.'
+                            "
+                            :disabled="workflow.deleted"
+                            full
+                            :version="workflow.version" />
+                    </BButtonGroup>
+                </div>
+            </div>
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Workflow/WorkflowRunButton.test.ts b/client/src/components/Workflow/WorkflowRunButton.test.ts
index 11c02dc95549..0aec407666a4 100644
--- a/client/src/components/Workflow/WorkflowRunButton.test.ts
+++ b/client/src/components/Workflow/WorkflowRunButton.test.ts
@@ -8,9 +8,10 @@ import WorkflowRunButton from "./WorkflowRunButton.vue";
 const localVue = getLocalVue();
 
 const WORKFLOW_ID = generateRandomString();
+const WORKFLOW_VERSION = 1;
 const WORKFLOW_RUN_BUTTON_SELECTOR = `[data-workflow-run="${WORKFLOW_ID}"]`;
 
-async function mountWorkflowRunButton(props?: { id: string; full?: boolean }) {
+async function mountWorkflowRunButton(props?: { id: string; version: number; full?: boolean }) {
     const wrapper = mount(WorkflowRunButton as object, {
         propsData: { ...props },
         localVue,
@@ -20,19 +21,12 @@ async function mountWorkflowRunButton(props?: { id: string; full?: boolean }) {
 }
 
 describe("WorkflowRunButton.vue", () => {
-    it("should render button with icon", async () => {
-        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID });
+    it("should render button with icon and route", async () => {
+        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID, version: WORKFLOW_VERSION });
 
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).exists()).toBeTruthy();
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).attributes("title")).toBe("Run workflow");
-        expect(wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR).text()).toBe("");
-    });
-
-    it("should redirect to workflow run page", async () => {
-        const { wrapper } = await mountWorkflowRunButton({ id: WORKFLOW_ID });
-
-        const runButton = await wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
-
-        expect(runButton.attributes("href")).toBe(`/workflows/run?id=${WORKFLOW_ID}`);
+        const button = wrapper.find(WORKFLOW_RUN_BUTTON_SELECTOR);
+        expect(button.attributes("title")).toBe("Run workflow");
+        expect(button.text()).toBe("");
+        expect(button.attributes("href")).toBe(`/workflows/run?id=${WORKFLOW_ID}&version=${WORKFLOW_VERSION}`);
     });
 });
diff --git a/client/src/components/Workflow/WorkflowRunButton.vue b/client/src/components/Workflow/WorkflowRunButton.vue
index 8d23de3c65c8..f5e26c981da9 100644
--- a/client/src/components/Workflow/WorkflowRunButton.vue
+++ b/client/src/components/Workflow/WorkflowRunButton.vue
@@ -1,12 +1,9 @@
 <script setup lang="ts">
-import { library } from "@fortawesome/fontawesome-svg-core";
 import { faPlay } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton } from "bootstrap-vue";
 import { computed } from "vue";
 
-library.add(faPlay);
-
 interface Props {
     id: string;
     full?: boolean;
@@ -14,9 +11,14 @@ interface Props {
     disabled?: boolean;
     version?: number;
     force?: boolean;
+    variant?: string;
 }
 
-const props = defineProps<Props>();
+const props = withDefaults(defineProps<Props>(), {
+    title: undefined,
+    version: undefined,
+    variant: "primary",
+});
 
 const runPath = computed(
     () => `/workflows/run?id=${props.id}${props.version !== undefined ? `&version=${props.version}` : ""}`
@@ -35,8 +37,9 @@ function forceRunPath() {
         v-b-tooltip.hover.top.html.noninteractive
         :title="title ?? 'Run workflow'"
         :data-workflow-run="id"
-        variant="primary"
+        :variant="variant"
         size="sm"
+        class="text-decoration-none"
         :disabled="disabled"
         :to="runPath"
         @click="forceRunPath">
diff --git a/client/src/components/WorkflowInvocationState/InvocationMessage.vue b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
index fdf447621b25..3759dfe82463 100644
--- a/client/src/components/WorkflowInvocationState/InvocationMessage.vue
+++ b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
@@ -20,6 +20,7 @@ type ReasonToLevel = {
     when_not_boolean: "error";
     unexpected_failure: "error";
     workflow_output_not_found: "warning";
+    workflow_parameter_invalid: "error";
 };
 
 const level: ReasonToLevel = {
@@ -34,6 +35,7 @@ const level: ReasonToLevel = {
     when_not_boolean: "error",
     unexpected_failure: "error",
     workflow_output_not_found: "warning",
+    workflow_parameter_invalid: "error",
 };
 
 const levelClasses = {
@@ -165,6 +167,10 @@ const infoString = computed(() => {
         return `Defined workflow output '${invocationMessage.output_name}' was not found in step ${
             invocationMessage.workflow_step_id + 1
         }.`;
+    } else if (reason === "workflow_parameter_invalid") {
+        return `Workflow parameter on step ${invocationMessage.workflow_step_id + 1} failed validation: ${
+            invocationMessage.details
+        }`;
     } else {
         return reason;
     }
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.test.ts b/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.test.ts
deleted file mode 100644
index eaabaad4015d..000000000000
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.test.ts
+++ /dev/null
@@ -1,155 +0,0 @@
-import { createTestingPinia } from "@pinia/testing";
-import { getFakeRegisteredUser } from "@tests/test-data";
-import { shallowMount } from "@vue/test-utils";
-import flushPromises from "flush-promises";
-import { getLocalVue } from "tests/jest/helpers";
-
-import sampleInvocation from "@/components/Workflow/test/json/invocation.json";
-import { useUserStore } from "@/stores/userStore";
-
-import WorkflowInvocationHeader from "./WorkflowInvocationHeader.vue";
-
-// Constants
-const WORKFLOW_OWNER = "test-user";
-const OTHER_USER = "other-user";
-const UNIMPORTABLE_WORKFLOW_ID = "invalid-workflow-id";
-const UNIMPORTABLE_WORKFLOW_INSTANCE_ID = "invalid-instance-id";
-const SAMPLE_WORKFLOW = {
-    id: "workflow-id",
-    name: "workflow-name",
-    owner: WORKFLOW_OWNER,
-    version: 1,
-};
-const IMPORT_ERROR_MESSAGE = "Failed to import workflow";
-
-const SELECTORS = {
-    INVOKED_WORKFLOW_HEADING: "anonymous-stub[h1='true']",
-    RETURN_TO_INVOCATIONS_LIST_BUTTON: "bbutton-stub[title='Return to Invocations List']",
-    ACTIONS_BUTTON_GROUP: "bbuttongroup-stub",
-    EDIT_WORKFLOW_BUTTON: `bbutton-stub[title='<b>Edit</b><br>${SAMPLE_WORKFLOW.name}']`,
-    IMPORT_WORKFLOW_BUTTON: "anonymous-stub[title='Import this workflow']",
-    RUN_WORKFLOW_BUTTON: `anonymous-stub[id='${SAMPLE_WORKFLOW.id}']`,
-    ALERT_MESSAGE: "balert-stub",
-};
-
-// Mock the copyWorkflow function for importing a workflow
-jest.mock("components/Workflow/workflows.services", () => ({
-    copyWorkflow: jest.fn().mockImplementation((workflowId: string) => {
-        if (workflowId === UNIMPORTABLE_WORKFLOW_ID) {
-            throw new Error(IMPORT_ERROR_MESSAGE);
-        }
-        return SAMPLE_WORKFLOW;
-    }),
-}));
-
-// Mock the workflow store to return the sample workflow
-jest.mock("@/stores/workflowStore", () => {
-    const originalModule = jest.requireActual("@/stores/workflowStore");
-    return {
-        ...originalModule,
-        useWorkflowStore: () => ({
-            ...originalModule.useWorkflowStore(),
-            getStoredWorkflowByInstanceId: jest.fn().mockImplementation((instanceId: string) => {
-                if (instanceId === UNIMPORTABLE_WORKFLOW_INSTANCE_ID) {
-                    return { ...SAMPLE_WORKFLOW, id: UNIMPORTABLE_WORKFLOW_ID };
-                }
-                return SAMPLE_WORKFLOW;
-            }),
-        }),
-    };
-});
-
-const localVue = getLocalVue();
-
-/**
- * Mounts the WorkflowInvocationHeader component with props/stores adjusted given the parameters
- * @param ownsWorkflow Whether the user owns the workflow associated with the invocation
- * @param hasReturnBtn Whether the component should have a return to invocations list button
- * @param unimportableWorkflow Whether the workflow import should fail
- * @returns The wrapper object
- */
-async function mountWorkflowInvocationHeader(ownsWorkflow = true, hasReturnBtn = false, unimportableWorkflow = false) {
-    const wrapper = shallowMount(WorkflowInvocationHeader as object, {
-        propsData: {
-            invocation: {
-                ...sampleInvocation,
-                workflow_id: !unimportableWorkflow ? sampleInvocation.workflow_id : UNIMPORTABLE_WORKFLOW_INSTANCE_ID,
-            },
-            invocationState: "scheduled",
-            isFullPage: true,
-            jobStatesSummary: {},
-            fromPanel: !hasReturnBtn,
-            invocationSchedulingTerminal: true,
-            invocationAndJobTerminal: true,
-        },
-        localVue,
-        pinia: createTestingPinia(),
-    });
-
-    const userStore = useUserStore();
-    userStore.currentUser = getFakeRegisteredUser({
-        username: ownsWorkflow ? WORKFLOW_OWNER : OTHER_USER,
-    });
-
-    return { wrapper };
-}
-
-describe("WorkflowInvocationHeader renders", () => {
-    // Included both cases in one test because these are always constant
-    it("(always) the workflow name in header and run button in actions", async () => {
-        const { wrapper } = await mountWorkflowInvocationHeader();
-
-        const heading = wrapper.find(SELECTORS.INVOKED_WORKFLOW_HEADING);
-        expect(heading.text()).toBe(`Invoked Workflow: "${SAMPLE_WORKFLOW.name}"`);
-
-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const runButton = actionsGroup.find(SELECTORS.RUN_WORKFLOW_BUTTON);
-        expect(runButton.attributes("title")).toContain(SAMPLE_WORKFLOW.name);
-    });
-
-    it("edit button if user owns the workflow", async () => {
-        const { wrapper } = await mountWorkflowInvocationHeader();
-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const editButton = actionsGroup.find(SELECTORS.EDIT_WORKFLOW_BUTTON);
-        expect(editButton.attributes("to")).toBe(
-            `/workflows/edit?id=${SAMPLE_WORKFLOW.id}&version=${SAMPLE_WORKFLOW.version}`
-        );
-    });
-
-    it("import button instead if user does not own the workflow", async () => {
-        const { wrapper } = await mountWorkflowInvocationHeader(false);
-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
-        expect(importButton.exists()).toBe(true);
-    });
-});
-
-describe("Importing a workflow in WorkflowInvocationHeader", () => {
-    it("should show a confirmation dialog when the import is successful", async () => {
-        const { wrapper } = await mountWorkflowInvocationHeader(false);
-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
-
-        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
-        await importButton.props().action();
-        await flushPromises();
-
-        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
-        expect(alert.attributes("variant")).toBe("info");
-        expect(alert.text()).toContain(`Workflow ${SAMPLE_WORKFLOW.name} imported successfully`);
-    });
-
-    it("should show an error dialog when the import fails", async () => {
-        const { wrapper } = await mountWorkflowInvocationHeader(false, false, true);
-        const actionsGroup = wrapper.find(SELECTORS.ACTIONS_BUTTON_GROUP);
-        const importButton = actionsGroup.find(SELECTORS.IMPORT_WORKFLOW_BUTTON);
-
-        // Cannot `.trigger("click")` on `AsyncButton` because it is a stubbed custom component
-        await importButton.props().action();
-        await flushPromises();
-
-        const alert = wrapper.find(SELECTORS.ALERT_MESSAGE);
-        expect(alert.attributes("variant")).toBe("danger");
-        expect(alert.text()).toContain(IMPORT_ERROR_MESSAGE);
-    });
-});
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.vue
deleted file mode 100644
index 9009597e72ad..000000000000
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationHeader.vue
+++ /dev/null
@@ -1,286 +0,0 @@
-<script setup lang="ts">
-import { faClock } from "@fortawesome/free-regular-svg-icons";
-import { faArrowLeft, faEdit, faExclamation, faHdd, faSitemap, faUpload } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BBadge, BButton, BButtonGroup } from "bootstrap-vue";
-import { storeToRefs } from "pinia";
-import { computed, ref } from "vue";
-import { RouterLink } from "vue-router";
-
-import { isRegisteredUser } from "@/api";
-import type { InvocationJobsSummary, InvocationStep, WorkflowInvocationElementView } from "@/api/invocations";
-import { useWorkflowInstance } from "@/composables/useWorkflowInstance";
-import { useHistoryStore } from "@/stores/historyStore";
-import { useUserStore } from "@/stores/userStore";
-import type { Workflow } from "@/stores/workflowStore";
-import localize from "@/utils/localization";
-import { errorMessageAsString } from "@/utils/simple-error";
-
-import { copyWorkflow } from "../Workflow/workflows.services";
-import {
-    errorCount as jobStatesSummaryErrorCount,
-    jobCount as jobStatesSummaryJobCount,
-    numTerminal,
-    okCount as jobStatesSummaryOkCount,
-    runningCount as jobStatesSummaryRunningCount,
-} from "./util";
-
-import AsyncButton from "../Common/AsyncButton.vue";
-import Heading from "../Common/Heading.vue";
-import SwitchToHistoryLink from "../History/SwitchToHistoryLink.vue";
-import ProgressBar from "../ProgressBar.vue";
-import UtcDate from "../UtcDate.vue";
-import WorkflowInvocationsCount from "../Workflow/WorkflowInvocationsCount.vue";
-import WorkflowRunButton from "../Workflow/WorkflowRunButton.vue";
-
-interface Props {
-    isFullPage?: boolean;
-    invocation: WorkflowInvocationElementView;
-    invocationState: string;
-    fromPanel?: boolean;
-    jobStatesSummary: InvocationJobsSummary;
-    invocationSchedulingTerminal: boolean;
-    invocationAndJobTerminal: boolean;
-    success?: boolean;
-    newHistoryTarget?: string;
-}
-
-const props = defineProps<Props>();
-
-const { workflow } = useWorkflowInstance(props.invocation.workflow_id);
-
-const { currentUser, isAnonymous } = storeToRefs(useUserStore());
-const owned = computed(() => {
-    if (isRegisteredUser(currentUser.value) && workflow.value) {
-        return currentUser.value.username === workflow.value.owner;
-    } else {
-        return false;
-    }
-});
-
-const importErrorMessage = ref<string | null>(null);
-const importedWorkflow = ref<Workflow | null>(null);
-
-async function onImport() {
-    if (!workflow.value || !workflow.value.owner) {
-        return;
-    }
-    try {
-        const wf = await copyWorkflow(workflow.value.id, workflow.value.owner);
-        importedWorkflow.value = wf as unknown as Workflow;
-    } catch (error) {
-        importErrorMessage.value = errorMessageAsString(error, "Failed to import workflow");
-    }
-}
-
-function getWorkflowName(): string {
-    return workflow.value?.name || "...";
-}
-
-type StepStateType = { [state: string]: number };
-
-const stepStates = computed<StepStateType>(() => {
-    const stepStates: StepStateType = {};
-    const steps: InvocationStep[] = props.invocation.steps || [];
-    for (const step of steps) {
-        if (!step) {
-            continue;
-        }
-        // the API defined state here allowing null and undefined is odd...
-        const stepState: string = step.state || "unknown";
-        if (!stepStates[stepState]) {
-            stepStates[stepState] = 1;
-        } else {
-            stepStates[stepState] += 1;
-        }
-    }
-    return stepStates;
-});
-
-const stepCount = computed<number>(() => {
-    return props.invocation.steps.length || 0;
-});
-
-const stepStatesStr = computed<string>(() => {
-    return `${stepStates.value?.scheduled || 0} of ${stepCount.value} steps successfully scheduled.`;
-});
-
-const okCount = computed<number>(() => {
-    return jobStatesSummaryOkCount(props.jobStatesSummary);
-});
-
-const runningCount = computed<number>(() => {
-    return jobStatesSummaryRunningCount(props.jobStatesSummary);
-});
-
-const jobCount = computed<number>(() => {
-    return jobStatesSummaryJobCount(props.jobStatesSummary);
-});
-
-const errorCount = computed<number>(() => {
-    return jobStatesSummaryErrorCount(props.jobStatesSummary);
-});
-
-const newCount = computed<number>(() => {
-    return jobCount.value - okCount.value - runningCount.value - errorCount.value;
-});
-
-const jobStatesStr = computed(() => {
-    let jobStr = `${numTerminal(props.jobStatesSummary) || 0} of ${jobCount.value} jobs complete`;
-    if (!props.invocationSchedulingTerminal) {
-        jobStr += " (total number of jobs will change until all steps fully scheduled)";
-    }
-    return `${jobStr}.`;
-});
-</script>
-
-<template>
-    <div>
-        <BAlert v-if="importErrorMessage" variant="danger" dismissible show @dismissed="importErrorMessage = null">
-            {{ importErrorMessage }}
-        </BAlert>
-        <BAlert v-else-if="importedWorkflow" variant="info" dismissible show @dismissed="importedWorkflow = null">
-            <span>
-                Workflow <b>{{ importedWorkflow.name }}</b> imported successfully.
-            </span>
-            <RouterLink to="/workflows/list">Click here</RouterLink> to view the imported workflow in the workflows
-            list.
-        </BAlert>
-        <div v-if="!props.success && props.isFullPage" class="d-flex flex-gapx-1">
-            <Heading h1 separator inline truncate size="xl" class="flex-grow-1">
-                Invoked Workflow: "{{ getWorkflowName() }}"
-            </Heading>
-
-            <div v-if="!props.fromPanel">
-                <BButton
-                    v-b-tooltip.hover.noninteractive
-                    :title="localize('Return to Invocations List')"
-                    class="text-nowrap"
-                    size="sm"
-                    variant="outline-primary"
-                    to="/workflows/invocations">
-                    <FontAwesomeIcon :icon="faArrowLeft" class="mr-1" />
-                    <span v-localize>Invocations List</span>
-                </BButton>
-            </div>
-        </div>
-        <div class="py-2 pl-3 d-flex justify-content-between align-items-center flex-nowrap">
-            <div v-if="props.isFullPage">
-                <i>
-                    <FontAwesomeIcon :icon="faClock" class="mr-1" />invoked
-                    <UtcDate :date="props.invocation.update_time" mode="elapsed" />
-                </i>
-                <span class="d-flex flex-gapx-1 align-items-center">
-                    <FontAwesomeIcon :icon="faHdd" />History:
-                    <SwitchToHistoryLink :history-id="props.invocation.history_id" />
-                    <BBadge
-                        v-if="props.newHistoryTarget && useHistoryStore().currentHistoryId !== props.newHistoryTarget"
-                        v-b-tooltip.hover.noninteractive
-                        data-description="new history badge"
-                        role="button"
-                        variant="info"
-                        title="Results generated in a new history. Click on history name to switch to that history.">
-                        <FontAwesomeIcon :icon="faExclamation" />
-                    </BBadge>
-                </span>
-            </div>
-            <div class="progress-bars mx-1">
-                <ProgressBar
-                    v-if="!stepCount"
-                    note="Loading step state summary..."
-                    :loading="true"
-                    class="steps-progress" />
-                <ProgressBar
-                    v-else-if="invocationState == 'cancelled'"
-                    note="Invocation scheduling cancelled - expected jobs and outputs may not be generated."
-                    :error-count="1"
-                    class="steps-progress" />
-                <ProgressBar
-                    v-else-if="invocationState == 'failed'"
-                    note="Invocation scheduling failed - Galaxy administrator may have additional details in logs."
-                    :error-count="1"
-                    class="steps-progress" />
-                <ProgressBar
-                    v-else
-                    :note="stepStatesStr"
-                    :total="stepCount"
-                    :ok-count="stepStates.scheduled"
-                    :loading="!invocationSchedulingTerminal"
-                    class="steps-progress" />
-                <ProgressBar
-                    :note="jobStatesStr"
-                    :total="jobCount"
-                    :ok-count="okCount"
-                    :running-count="runningCount"
-                    :new-count="newCount"
-                    :error-count="errorCount"
-                    :loading="!invocationAndJobTerminal"
-                    class="jobs-progress" />
-            </div>
-            <div v-if="workflow" class="d-flex flex-gapx-1 align-items-center">
-                <div class="d-flex flex-column align-items-end mr-2">
-                    <span v-if="workflow.version !== undefined" class="mb-1">
-                        <FontAwesomeIcon :icon="faSitemap" />
-                        Workflow Version: {{ workflow.version + 1 }}
-                    </span>
-                    <WorkflowInvocationsCount class="float-right" :workflow="workflow" />
-                </div>
-                <BButtonGroup vertical>
-                    <BButton
-                        v-if="owned"
-                        v-b-tooltip.hover.noninteractive.html
-                        :title="
-                            !workflow.deleted
-                                ? `<b>Edit</b><br>${getWorkflowName()}`
-                                : 'This workflow has been deleted.'
-                        "
-                        size="sm"
-                        variant="secondary"
-                        :disabled="workflow.deleted"
-                        :to="`/workflows/edit?id=${workflow.id}&version=${workflow.version}`">
-                        <FontAwesomeIcon :icon="faEdit" />
-                        <span v-localize>Edit</span>
-                    </BButton>
-                    <AsyncButton
-                        v-else
-                        v-b-tooltip.hover.noninteractive
-                        size="sm"
-                        :disabled="isAnonymous"
-                        :title="localize('Import this workflow')"
-                        :icon="faUpload"
-                        variant="outline-primary"
-                        :action="onImport">
-                        <span v-localize>Import</span>
-                    </AsyncButton>
-                    <WorkflowRunButton
-                        :id="workflow.id || ''"
-                        :title="
-                            !workflow.deleted
-                                ? `<b>Rerun</b><br>${getWorkflowName()}`
-                                : 'This workflow has been deleted.'
-                        "
-                        :disabled="workflow.deleted"
-                        full
-                        force
-                        :version="workflow.version" />
-                </BButtonGroup>
-            </div>
-        </div>
-    </div>
-</template>
-
-<style scoped lang="scss">
-.progress-bars {
-    // progress bar shrinks to fit divs on either side
-    flex-grow: 1;
-    flex-shrink: 1;
-    max-width: 50%;
-
-    .steps-progress,
-    .jobs-progress {
-        // truncate text in progress bars
-        white-space: nowrap;
-        overflow: hidden;
-    }
-}
-</style>
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
index 33af070b8c88..299b1227a9a1 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue
@@ -4,7 +4,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton, BNavItem, BTab, BTabs } from "bootstrap-vue";
 import { computed, onUnmounted, ref, watch } from "vue";
 
-import { type InvocationJobsSummary, type WorkflowInvocationElementView } from "@/api/invocations";
+import { type InvocationJobsSummary, type InvocationStep, type WorkflowInvocationElementView } from "@/api/invocations";
 import { useAnimationFrameResizeObserver } from "@/composables/sensors/animationFrameResizeObserver";
 import { getRootFromIndexLink } from "@/onload";
 import { useInvocationStore } from "@/stores/invocationStore";
@@ -12,12 +12,21 @@ import { useWorkflowStore } from "@/stores/workflowStore";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 import { cancelWorkflowScheduling } from "./services";
-import { isTerminal, jobCount, runningCount } from "./util";
+import {
+    errorCount as jobStatesSummaryErrorCount,
+    isTerminal,
+    jobCount as jobStatesSummaryJobCount,
+    numTerminal,
+    okCount as jobStatesSummaryOkCount,
+    runningCount as jobStatesSummaryRunningCount,
+} from "./util";
 
+import ProgressBar from "../ProgressBar.vue";
 import WorkflowInvocationSteps from "../Workflow/Invocation/Graph/WorkflowInvocationSteps.vue";
 import InvocationReport from "../Workflow/InvocationReport.vue";
+import WorkflowAnnotation from "../Workflow/WorkflowAnnotation.vue";
+import WorkflowNavigationTitle from "../Workflow/WorkflowNavigationTitle.vue";
 import WorkflowInvocationExportOptions from "./WorkflowInvocationExportOptions.vue";
-import WorkflowInvocationHeader from "./WorkflowInvocationHeader.vue";
 import WorkflowInvocationInputOutputTabs from "./WorkflowInvocationInputOutputTabs.vue";
 import WorkflowInvocationMetrics from "./WorkflowInvocationMetrics.vue";
 import WorkflowInvocationOverview from "./WorkflowInvocationOverview.vue";
@@ -27,14 +36,12 @@ interface Props {
     invocationId: string;
     isSubworkflow?: boolean;
     isFullPage?: boolean;
-    fromPanel?: boolean;
     success?: boolean;
-    newHistoryTarget?: string;
+    newHistoryTarget?: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     isSubworkflow: false,
-    newHistoryTarget: undefined,
 });
 
 const emit = defineEmits<{
@@ -69,10 +76,8 @@ const disabledReportTooltip = computed(() => {
     const state = invocationState.value;
     if (state != "scheduled") {
         return `This workflow is not currently scheduled. The current state is ${state}. Once the workflow is fully scheduled and jobs have complete this option will become available.`;
-    } else if (runningCount(jobStatesSummary.value) != 0) {
-        return `The workflow invocation still contains ${runningCount(
-            jobStatesSummary.value
-        )} running job(s). Once these jobs have completed this option will become available.`;
+    } else if (runningCount.value != 0) {
+        return `The workflow invocation still contains ${runningCount.value} running job(s). Once these jobs have completed this option will become available.`;
     } else {
         return "Steps for this workflow are still running. A report will be available once complete.";
     }
@@ -100,7 +105,7 @@ const invocationSchedulingTerminal = computed(() => {
     );
 });
 const jobStatesTerminal = computed(() => {
-    if (invocationSchedulingTerminal.value && jobCount(jobStatesSummary.value as InvocationJobsSummary) === 0) {
+    if (invocationSchedulingTerminal.value && jobCount.value === 0) {
         // no jobs for this invocation (think subworkflow or just inputs)
         return true;
     }
@@ -111,11 +116,63 @@ const jobStatesSummary = computed(() => {
     return (!jobsSummary ? null : jobsSummary) as InvocationJobsSummary;
 });
 const invocationStateSuccess = computed(() => {
-    return (
-        invocationState.value == "scheduled" &&
-        runningCount(jobStatesSummary.value) === 0 &&
-        invocationAndJobTerminal.value
-    );
+    return invocationState.value == "scheduled" && runningCount.value === 0 && invocationAndJobTerminal.value;
+});
+
+type StepStateType = { [state: string]: number };
+
+const stepStates = computed<StepStateType>(() => {
+    const stepStates: StepStateType = {};
+    const steps: InvocationStep[] = invocation.value?.steps || [];
+    for (const step of steps) {
+        if (!step) {
+            continue;
+        }
+        // the API defined state here allowing null and undefined is odd...
+        const stepState: string = step.state || "unknown";
+        if (!stepStates[stepState]) {
+            stepStates[stepState] = 1;
+        } else {
+            stepStates[stepState] += 1;
+        }
+    }
+    return stepStates;
+});
+
+const stepCount = computed<number>(() => {
+    return invocation.value?.steps.length || 0;
+});
+
+const stepStatesStr = computed<string>(() => {
+    return `${stepStates.value?.scheduled || 0} of ${stepCount.value} steps successfully scheduled.`;
+});
+
+const okCount = computed<number>(() => {
+    return jobStatesSummaryOkCount(jobStatesSummary.value);
+});
+
+const errorCount = computed<number>(() => {
+    return jobStatesSummaryErrorCount(jobStatesSummary.value);
+});
+
+const runningCount = computed<number>(() => {
+    return jobStatesSummaryRunningCount(jobStatesSummary.value);
+});
+
+const jobCount = computed<number>(() => {
+    return jobStatesSummaryJobCount(jobStatesSummary.value);
+});
+
+const newCount = computed<number>(() => {
+    return jobCount.value - okCount.value - runningCount.value - errorCount.value;
+});
+
+const jobStatesStr = computed(() => {
+    let jobStr = `${numTerminal(jobStatesSummary.value) || 0} of ${jobCount.value} jobs complete`;
+    if (!invocationSchedulingTerminal.value) {
+        jobStr += " (total number of jobs will change until all steps fully scheduled)";
+    }
+    return `${jobStr}.`;
 });
 
 const workflowStore = useWorkflowStore();
@@ -171,16 +228,52 @@ function cancelWorkflowSchedulingLocal() {
 
 <template>
     <div v-if="invocation" class="d-flex flex-column w-100" data-description="workflow invocation state">
-        <WorkflowInvocationHeader
-            :is-full-page="props.isFullPage"
+        <WorkflowNavigationTitle
+            v-if="props.isFullPage && !props.success"
             :invocation="invocation"
-            :invocation-state="invocationState"
-            :from-panel="props.fromPanel"
-            :job-states-summary="jobStatesSummary"
-            :success="props.success"
-            :new-history-target="props.newHistoryTarget"
-            :invocation-scheduling-terminal="invocationSchedulingTerminal"
-            :invocation-and-job-terminal="invocationAndJobTerminal" />
+            :workflow-id="invocation.workflow_id" />
+        <WorkflowAnnotation
+            v-if="props.isFullPage"
+            :workflow-id="invocation.workflow_id"
+            :invocation-update-time="invocation.update_time"
+            :history-id="invocation.history_id"
+            :new-history-target="props.newHistoryTarget">
+            <template v-slot:middle-content>
+                <div class="progress-bars mx-1">
+                    <ProgressBar
+                        v-if="!stepCount"
+                        note="Loading step state summary..."
+                        :loading="true"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else-if="invocationState == 'cancelled'"
+                        note="Invocation scheduling cancelled - expected jobs and outputs may not be generated."
+                        :error-count="1"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else-if="invocationState == 'failed'"
+                        note="Invocation scheduling failed - Galaxy administrator may have additional details in logs."
+                        :error-count="1"
+                        class="steps-progress" />
+                    <ProgressBar
+                        v-else
+                        :note="stepStatesStr"
+                        :total="stepCount"
+                        :ok-count="stepStates.scheduled"
+                        :loading="!invocationSchedulingTerminal"
+                        class="steps-progress" />
+                    <ProgressBar
+                        :note="jobStatesStr"
+                        :total="jobCount"
+                        :ok-count="okCount"
+                        :running-count="runningCount"
+                        :new-count="newCount"
+                        :error-count="errorCount"
+                        :loading="!invocationAndJobTerminal"
+                        class="jobs-progress" />
+                </div>
+            </template>
+        </WorkflowAnnotation>
         <BTabs
             ref="invocationTabs"
             class="mt-1 d-flex flex-column overflow-auto"
@@ -271,3 +364,19 @@ function cancelWorkflowSchedulingLocal() {
         <span v-localize>Invocation not found.</span>
     </BAlert>
 </template>
+
+<style scoped lang="scss">
+.progress-bars {
+    // progress bar shrinks to fit divs on either side
+    flex-grow: 1;
+    flex-shrink: 1;
+    max-width: 50%;
+
+    .steps-progress,
+    .jobs-progress {
+        // truncate text in progress bars
+        white-space: nowrap;
+        overflow: hidden;
+    }
+}
+</style>
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 011bb9ffd082..862a0622cc5f 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -656,7 +656,6 @@ export function getRouter(Galaxy) {
                         props: (route) => ({
                             invocationId: route.params.invocationId,
                             isFullPage: true,
-                            fromPanel: Boolean(route.query.from_panel),
                         }),
                     },
                     {
diff --git a/client/src/nls/ja/locale.js b/client/src/nls/ja/locale.js
index 02208bbf63f5..54205bf383ab 100644
--- a/client/src/nls/ja/locale.js
+++ b/client/src/nls/ja/locale.js
@@ -77,7 +77,7 @@ define({
     // ---- history-view
     "This history is empty": "ヒストリーは空です",
     "No matching datasets found": "一致するデータセットが見つかりませんでした",
-    //"An error occurred while getting updates from the server" :
+    "An error occurred while getting updates from the server": "サーバーから更新を取得中にエラーが起こりました",
     //false,
     //"Please contact a Galaxy administrator if the problem persists" :
     //false,
@@ -87,7 +87,8 @@ define({
     "Search datasets": "データセットを検索する",
     "You are currently viewing a deleted history!": "消去したヒストリーをみています。",
     "You are over your disk quota": "あなたはディスククォータを超えている",
-    //"Tool execution is on hold until your disk usage drops below your allocated quota" :
+    "Tool execution is on hold until your disk usage drops below your allocated quota":
+        "ディスク使用料があなたに割り当てられたクォータを下回るまでツールの実行は停止します",
     //false,
     All: "一式",
     None: "なし",
@@ -99,13 +100,13 @@ define({
     "Click to rename history": "ヒストリーの名前を変更するにはクリック",
     // multi operations
     "Operations on multiple datasets": "複数のデータセットに対する操作",
-    //"Hide datasets" :
+    "Hide datasets": "データセットを隠す",
     //false,
-    //"Unhide datasets" :
+    "Unhide datasets": "隠れたデータセットの回復",
     //false,
-    //"Delete datasets" :
+    "Delete datasets": "データセットの削除",
     //false,
-    //"Undelete datasets" :
+    "Undelete datasets": "削除されたデータセットの回復",
     //false,
     "Permanently delete datasets": "永久にデータセットを削除",
     "This will permanently remove the data in your datasets. Are you sure?":
@@ -113,7 +114,7 @@ define({
 
     // ---- history-view-annotated
     Dataset: "データセット",
-    //"Annotation" :
+    Annotation: "アノテーション",
     //false,
 
     // ---- history-view-edit-current
@@ -123,53 +124,56 @@ define({
     //TODO:
     //"You can <% loadYourOwn %> or <% externalSource %>" :
     //false,
-    //"load your own data" :
+    "load your own data": "自分のデータをロード",
     //false,
-    //"get data from an external source" :
+    "get data from an external source": "外部のソースからデータを取得",
     //false,
 
     // these aren't in zh/ginga.po and the template doesn't localize
-    //"Include Deleted Datasets" :
+    "Include Deleted Datasets": "削除されたデータセットを含める",
     //false,
-    //"Include Hidden Datasets" :
+    "Include Hidden Datasets": "隠れたデータセットを含める",
     //false,
 
     // ---------------------------------------------------------------------------- datasets
     // ---- hda-model
-    //"Unable to purge dataset" :
+    "Unable to purge dataset": "データセットを完全削除出来ません",
     //false,
 
     // ---- hda-base
     // display button
-    //"Cannot display datasets removed from disk" :
+    "Cannot display datasets removed from disk": "ディスクから消去されたデータは表示できません",
     //false,
-    //"This dataset must finish uploading before it can be viewed" :
+    "This dataset must finish uploading before it can be viewed":
+        "このデータセットは見る前にアップロードが完了する必要があります",
     //false,
-    //"This dataset is not yet viewable" :
+    "This dataset is not yet viewable": "このデータセットはまだ見ることができません",
     //false,
     "View data": "データを表示",
     // download button
     Download: "ダウンロード",
     "Download dataset": "データセットをダウンロード",
-    //"Additional files" :
+    "Additional files": "追加のファイル",
     //false,
     // info/show_params
     "View details": "細部を表示",
 
     // dataset states
     // state: new
-    //"This is a new dataset and not all of its data are available yet" :
+    "This is a new dataset and not all of its data are available yet":
+        "これは新しいデータセットですが、まだすべてのデータが利用可能にはなっていません",
     //false,
     // state: noPermission
-    //"You do not have permission to view this dataset" :
+    "You do not have permission to view this dataset": "このデータセットを見るための権限がありません",
     //false,
     // state: discarded
-    //"The job creating this dataset was cancelled before completion" :
+    "The job creating this dataset was cancelled before completion":
+        "このデータセットを作成するジョブは、完了する前にキャンセルされました",
     //false,
     // state: queued
     "This job is waiting to run": "ジョブは実行待ちです",
     // state: upload
-    //"This dataset is currently uploading" :
+    "This dataset is currently uploading": "このデータセットは現在アップロード中です",
     //false,
     // state: setting_metadata
     //"Metadata is being auto-detected" :
@@ -184,11 +188,12 @@ define({
     // state: empty
     "No data": "データ無し",
     // state: failed_metadata
-    //"An error occurred setting the metadata for this dataset" :
+    "An error occurred setting the metadata for this dataset":
+        "このデータセットのメタデータを設定する際にエラーがでました",
     //false,
 
     // ajax error prefix
-    //"There was an error getting the data for this dataset" :
+    "There was an error getting the data for this dataset": "このデータセットのデータを取得する際にエラーがでました",
     //false,
 
     // purged'd/del'd msg
@@ -201,17 +206,18 @@ define({
 
     // ---- hda-edit
     "Edit attributes": "変数を編集する",
-    //"Cannot edit attributes of datasets removed from disk" :
+    "Cannot edit attributes of datasets removed from disk": "ディスクから削除されたデータセットの属性は編集できない",
     //false,
     //"Undelete dataset to edit attributes" :
     //false,
-    //"This dataset must finish uploading before it can be edited" :
+    "This dataset must finish uploading before it can be edited":
+        "このデータセットは編集する前にアップロードが完了する必要がある",
     //false,
-    //"This dataset is not yet editable" :
+    "This dataset is not yet editable": "このデータセットは、まだ編集可能ではない",
     //false,
 
     Delete: "削除する",
-    //"Dataset is already deleted" :
+    "Dataset is already deleted": "データセットは、既に削除されている",
     //false,
 
     "View or report this error": "このエラーを届け出る",
@@ -233,9 +239,9 @@ define({
     //"set it manually or retry auto-detection" :
     //false,
 
-    //"Edit dataset tags" :
+    "Edit dataset tags": "データセットのタグを編集",
     //false,
-    //"Edit dataset annotation" :
+    "Edit dataset annotation": "データセットのアノテーションを編集",
     //false,
 
     // ---------------------------------------------------------------------------- admin
@@ -266,11 +272,11 @@ define({
     Data: "データ",
     "Form Definitions": "フォーム定義",
     // ---------------------------------------------------------------------------- misc. MVC
-    //"Tags" :
+    Tags: "タグ",
     //false,
-    //"Annotation" :
+    Annotation: "アノテーション",
     //false,
-    //"Edit annotation" :
+    "Edit annotation": "アノテーションを編集",
     //false,
     "Your workflows": "あなたのワークフロー",
 });
diff --git a/client/src/stores/workflowStore.ts b/client/src/stores/workflowStore.ts
index f1bc4a606c71..e68b62ab604f 100644
--- a/client/src/stores/workflowStore.ts
+++ b/client/src/stores/workflowStore.ts
@@ -15,6 +15,9 @@ export interface Workflow {
     version: number;
     deleted?: boolean;
     owner?: string;
+    annotation?: string;
+    tags?: string[];
+    update_time?: string;
 }
 
 export const useWorkflowStore = defineStore("workflowStore", () => {
diff --git a/config/plugins/visualizations/annotate_image/config/annotate_image.xml b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
index 0e6781078cf0..b5bcfe76a7ab 100644
--- a/config/plugins/visualizations/annotate_image/config/annotate_image.xml
+++ b/config/plugins/visualizations/annotate_image/config/annotate_image.xml
@@ -13,5 +13,5 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="jquery.contextMenu.css"/>
+    <entry_point entry_point_type="script" src="script.js" css="jquery.contextMenu.css"/>
 </visualization>
diff --git a/config/plugins/visualizations/annotate_image/package.json b/config/plugins/visualizations/annotate_image/package.json
index f546269cf52a..ae7cd6a66da9 100644
--- a/config/plugins/visualizations/annotate_image/package.json
+++ b/config/plugins/visualizations/annotate_image/package.json
@@ -19,7 +19,7 @@
     },
     "scripts": {
         "build": "yarn build-css && yarn build-js",
-        "build-css": "cp 'node_modules/jquery-contextmenu/dist/jquery.contextMenu.css' 'static/'",
+        "build-css": "cp -f 'node_modules/jquery-contextmenu/dist/jquery.contextMenu.css' 'static/'",
         "build-js": "parcel build src/script.js --dist-dir static"
     }
 }
diff --git a/config/plugins/visualizations/annotate_image/src/script.js b/config/plugins/visualizations/annotate_image/src/script.js
index 443c1932b6cf..b90b3cb1901d 100644
--- a/config/plugins/visualizations/annotate_image/src/script.js
+++ b/config/plugins/visualizations/annotate_image/src/script.js
@@ -5,12 +5,6 @@ import _ from "underscore";
 // Use lighter weight 'core' version of paper since we don't need paperscript
 import paper from "../node_modules/paper/dist/paper-core.js";
 
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
 const CommandManager = (function () {
     function CommandManager() {}
 
@@ -60,10 +54,7 @@ const generateUUID = function () {
     return uuid;
 };
 
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (opt) {
-    const chart = opt.chart;
-    const dataset = opt.dataset;
+function render(downloadUrl) {
     const defaults = { color: "red", width: 4, opacity: 0.5 };
     $.fn.createCanvas = function (options) {
         let settings = $.extend({}, defaults, options || {});
@@ -441,17 +432,13 @@ window.bundleEntries.load = function (opt) {
         });
     };
 
-    const downloadUrl = prefixedDownloadUrl(opt.root, dataset.download_url);
-
     fetch(downloadUrl)
         .then((response) => {
             if (!response.ok) {
                 throw new Error("Failed to access dataset.");
             }
-            return response.text();
-        })
-        .then((content) => {
-            const $chartViewer = $("#" + opt.target);
+
+            const $chartViewer = $("#app");
             $chartViewer.html("<img id='image-annotate' src='" + downloadUrl + "' />");
             $chartViewer.css("overflow", "auto");
             $chartViewer.css("position", "relative");
@@ -470,12 +457,16 @@ window.bundleEntries.load = function (opt) {
                     img_height: height,
                 });
             });
-
-            chart.state("ok", "Chart drawn.");
-            opt.process.resolve();
         })
         .catch((error) => {
-            chart.state("failed", error.message);
-            opt.process.resolve();
+            console.error(error.message);
         });
 };
+
+const { root, visualization_config } = JSON.parse(document.getElementById("app").dataset.incoming);
+
+const datasetId = visualization_config.dataset_id;
+
+const downloadUrl = window.location.origin + root + "api/datasets/" + datasetId + "/display";
+
+render(downloadUrl);
diff --git a/config/plugins/visualizations/cytoscape/config/cytoscape.xml b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
index b73ec2e8728b..9cd91fdeb459 100644
--- a/config/plugins/visualizations/cytoscape/config/cytoscape.xml
+++ b/config/plugins/visualizations/cytoscape/config/cytoscape.xml
@@ -13,7 +13,10 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js"/>
+    <requirements>
+        <requirement type="npm" version="0.0.2" package="@galaxyproject/cytoscape"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
         <input>
             <label>Curve style</label>
@@ -69,10 +72,6 @@
                     <label>Grid</label>
                     <value>grid</value>
                 </data>
-                <data>
-                    <label>Null</label>
-                    <value>null</value>
-                </data>
                 <data>
                     <label>Preset</label>
                     <value>preset</value>
@@ -87,18 +86,7 @@
             <label>Directed/Undirected</label>
             <name>directed</name>
             <help>Select a kind of edge.</help>
-            <type>select</type>
-            <display>radio</display>
-            <data>
-                <data>
-                    <label>Directed</label>
-                    <value>triangle</value>
-                </data>
-                <data>
-                    <label>Undirected</label>
-                    <value></value>
-                </data>
-            </data>
+            <type>boolean</type>
         </input>
         <input>
             <label>Graph algorithms</label>
@@ -115,10 +103,6 @@
                     <label>Depth First Search</label>
                     <value>dfs</value>
                 </data>
-                <data>
-                    <label>Depth First Search</label>
-                    <value>dfs</value>
-                </data>
                 <data>
                     <label>Minimum Spanning Tree (Kruskal)</label>
                     <value>kruskal</value>
diff --git a/config/plugins/visualizations/cytoscape/package.json b/config/plugins/visualizations/cytoscape/package.json
deleted file mode 100644
index 09a404bb7918..000000000000
--- a/config/plugins/visualizations/cytoscape/package.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.1.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "cytoscape": "^3.2.8",
-        "jquery": "^3.1.1"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "^2.12.0"
-    }
-}
diff --git a/config/plugins/visualizations/cytoscape/src/script.js b/config/plugins/visualizations/cytoscape/src/script.js
deleted file mode 100644
index a2d0fdd2d010..000000000000
--- a/config/plugins/visualizations/cytoscape/src/script.js
+++ /dev/null
@@ -1,279 +0,0 @@
-import Cytoscape from 'cytoscape';
-
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
-// Public method. Return graph data as JSON
-var parse_sif = function( text ) {
-    // Private variables and methods
-    var nodes = {}, links = {}, content = [];
-
-    // Add a node
-    var _getNode = function( id ) {
-        if(!nodes[id]) {
-            nodes[id] = {id: id};
-        }
-        return nodes[id];
-    };
-
-    // Parse each line of the SIF file
-    var _parse = function( line, i ) {
-        var source, interaction, j, length;
-        line = ( line.split('\t').length > 1 ) ? line.split('\t') : line.split(' ');
-        source = _getNode( line[0] );
-        interaction = ( line[1] ? line[1] : "" );
-        if( line.length && line.length > 0 && line[0] !== "" ) {
-            if( interaction !== "" ) {
-                // Get all the target nodes for a source
-                for ( j = 2, length = line.length; j < length; j++ ) {
-                    if( line[j] !== "" ) {
-                        // Create an object for each target for the source
-                        var target = _getNode( line[j] ),
-                        relation_object = {target: target.id,
-                            source: source.id,
-                            id: source.id + target.id,
-                            relation: interaction.replace(/[''""]+/g, '') }; // Replace quotes in relation
-                        if( source < target ) {
-                            links[ source.id + target.id + interaction ] = relation_object;
-                        } else {
-                            links[ target.id + source.id + interaction ] = relation_object;
-                        }
-                    }
-                }
-            }
-            // Handle the case of single node i.e. no relation with any other node
-            // and only the source exists
-            else {
-                links[ source.id ] = { target: "", source: source.id, id: source.id, relation: "" };
-            }
-        }
-    };
-
-    // Convert to array from objects
-    var _toArr = function( obj ) {
-        var arr = [];
-        for (var key in obj) {
-            arr.push( obj[key] );
-        }
-        return arr;
-    };
-
-    // Make content from list of nodes and links
-    var _toDataArr = function( nodes, links ) {
-        var content = [], node_length, links_length;
-        // Make a list of all nodes
-        for(var i = 0, node_length = nodes.length; i < node_length; i++) {
-            content.push( { 'data': nodes[i] } );
-        }
-        // Make a list of all relationships among nodes
-        for(var i = 0, links_length = links.length; i < links_length; i++) {
-            content.push( { 'data': links[i] } );
-        }
-        return content;
-    };
-
-    var lines = text.split('\n'), i, length, nodesarr, linksarr;
-    for ( i = 0, length = lines.length; i < length; i++ ) {
-        if( lines[i] !== "" ) {
-            _parse( lines[i], i );
-        }
-    }
-    nodesarr = _toArr( nodes );
-    linksarr = _toArr( links );
-    return { content: _toDataArr( nodesarr, linksarr ) };
-};
-
-function run_search_algorithm( cytoscape, root_id, type, self ) {
-    var algorithm = "", i = 0;
-    var selectNextElement = function() {
-        if( i < algorithm.path.length ) {
-            // Add css class for the selected edge(s)
-            algorithm.path[i].addClass( 'searchpath' );
-            i++;
-            // Animate the edges and nodes coloring
-            // of the path with a delay of 500ms
-            setTimeout( selectNextElement, 500 );
-        }
-    };
-    switch( type ) {
-        // Breadth First Search
-        case "bfs":
-            algorithm = cytoscape.elements().bfs( '#' + root_id, function() { }, true );
-            selectNextElement();
-            break;
-        // Depth First Search
-        case "dfs":
-            algorithm = cytoscape.elements().dfs( '#' + root_id, function() { }, true );
-            selectNextElement();
-            break;
-        // A* search
-        case "astar":
-            // Choose root and destination for performing A*
-            if( !self.astar_root ) {
-                self.astar_root = root_id;
-            }
-            else {
-                self.astar_destination = root_id;
-            }
-            if( self.astar_root && self.astar_destination ) {
-                algorithm = cytoscape.elements().aStar({ root: "#" + self.astar_root, goal: "#" + self.astar_destination },function() {}, true);
-                selectNextElement();
-            }
-         default:
-            return;
-    }
-};
-
-function run_traversal_type( cytoscape, root_id, type ) {
-    var node_collection;
-    switch( type ) {
-        // Recursively get edges (and their sources) coming into the nodes in a collection
-        case "predecessors":
-             node_collection = cytoscape.$( '#' + root_id ).predecessors();
-             break;
-        // Recursively get edges (and their targets) coming out of the nodes in a collection
-        case "successors":
-             node_collection = cytoscape.$( '#' + root_id ).successors();
-             break;
-        // Get edges (and their targets) coming out of the nodes in a collection.
-        case "outgoers":
-             node_collection = cytoscape.$( '#' + root_id ).outgoers();
-             break;
-        // Get edges (and their sources) coming into the nodes in a collection.
-        case "incomers":
-             node_collection = cytoscape.$( '#' + root_id ).incomers();
-             break;
-        // From the set of calling nodes, get the nodes which are roots
-        case "roots":
-             node_collection = cytoscape.$( '#' + root_id ).roots();
-             break;
-        // From the set of calling nodes, get the nodes which are leaves
-        case "leaves":
-             node_collection = cytoscape.$( '#' + root_id ).leaves();
-             break;
-        default:
-             return;
-    }
-    // Add CSS class for selected nodes and edges
-    node_collection.edges().addClass( 'searchpath' );
-    node_collection.nodes().addClass( 'searchpath' );
-};
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    var self = this,
-    chart    = options.chart,
-    dataset  = options.dataset,
-    settings = options.chart.settings,
-    data_content = null,
-    cytoscape = null,
-    sif_file_ext = "sif",
-    highlighted_color = settings.get( 'color_picker_highlighted' );
-    $.ajax({
-        url     : prefixedDownloadUrl(options.root, dataset.download_url),
-        success : function( content ) {
-            // Select data for the graph
-            if( dataset.file_ext === sif_file_ext ) {
-                data_content = parse_sif( content ).content;
-            }
-            else {
-                data_content = content.elements ? content.elements : content;
-            }
-            try {
-                cytoscape = Cytoscape({
-                    container: document.getElementById( options.target ),
-                    layout: {
-                        name: settings.get( 'layout_name' ),
-                        idealEdgeLength: 100,
-                        nodeOverlap: 20
-                    },
-                    minZoom: 0.1,
-                    maxZoom: 20,
-                    style: [{
-                        selector: 'node',
-                        style: {
-                            'background-color': settings.get( 'color_picker_nodes' ),
-                            'opacity': 1,
-                            'content': 'data(id)',
-                            'text-valign': 'center',
-                        }
-                    },
-                    {
-                        selector: 'core',
-                        style: {
-                                'selection-box-color':'#AAD8FF',
-                                'selection-box-border-color':'#8BB0D0',
-                                'selection-box-opacity':'0.5'
-                        }
-                    },
-                    {
-                        selector: 'edge',
-                        style: {
-                            'curve-style': settings.get( 'curve_style' ),
-                            'haystack-radius': 0,
-                            'width': 3,
-                            'opacity': 1,
-                            'line-color': settings.get( 'color_picker_edges' ),
-                            'target-arrow-shape': settings.get( 'directed' ),
-                            "overlay-padding":"3px"
-                        }
-                    },
-                    {
-                        selector:'node:selected',
-                        style: {
-                            "border-width": "6px",
-                            "border-color": "#AAD8FF",
-                            "border-opacity": "0.5",
-                            "background-color": "#77828C",
-                            "text-outline-color": "#77828C"
-                        }
-                    },
-                    {
-                        selector: '.searchpath',
-                        style: {
-                            'background-color': highlighted_color,
-                            'line-color': highlighted_color,
-                            'target-arrow-color': highlighted_color,
-                            'transition-property': 'background-color, line-color, target-arrow-color',
-                            'transition-duration': '0.5s'
-                    }
-                    }],
-                    elements: data_content // Set the JSON data for viewing
-                });
-                // Highlight the minimum spanning tree found using Kruskal algorithm
-                if( settings.get( 'search_algorithm' ) === "kruskal" ) {
-                    var kruskal = cytoscape.elements().kruskal();
-                    kruskal.edges().addClass( 'searchpath' );
-                }
-                // Register tap (clicking a node) event on graph nodes
-                // On tapping any node, BFS or DFS start from that node
-                cytoscape.$( 'node' ).on('tap', function( e ) {
-                    var ele = e.cyTarget,
-                        search_algorithm = settings.get( 'search_algorithm' ),
-                        traversal_type = settings.get( 'graph_traversal' );
-                    // If search algorithm and traversal both are chosen,
-                    // search algorithm will take preference
-                    if( settings.get( 'search_algorithm' ) !== "" ) {
-                        run_search_algorithm( cytoscape, ele.id(), search_algorithm, self );
-                    }
-                    else if( settings.get( 'graph_traversal' ) !== "" ) {
-                        run_traversal_type( cytoscape, ele.id(), traversal_type );
-                    }
-                });
-                chart.state( 'ok', 'Chart drawn.' );
-                // Re-renders the graph view when window is resized
-                $( window ).resize( function() { cytoscape.layout(); } );
-            } catch( err ) {
-                chart.state( 'failed', err );
-            }
-            options.process.resolve();
-        },
-        error: function() {
-            chart.state( 'failed', 'Failed to access dataset.' );
-            options.process.resolve();
-        }
-    });
-};
diff --git a/config/plugins/visualizations/cytoscape/static/logo.png b/config/plugins/visualizations/cytoscape/static/logo.png
index ce891f674bb8..4c49f1d32aa8 100644
Binary files a/config/plugins/visualizations/cytoscape/static/logo.png and b/config/plugins/visualizations/cytoscape/static/logo.png differ
diff --git a/config/plugins/visualizations/example/static/script.js b/config/plugins/visualizations/example/static/script.js
index e17270b74957..262765a01502 100644
--- a/config/plugins/visualizations/example/static/script.js
+++ b/config/plugins/visualizations/example/static/script.js
@@ -1,4 +1,4 @@
-const { visualization_config, visualization_plugin, root } = JSON.parse(document.getElementById("app").dataset.incoming);
+const { root, visualization_config, visualization_plugin } = JSON.parse(document.getElementById("app").dataset.incoming);
 
 const div = Object.assign(document.createElement("div"), {
     style: "border: 2px solid #25537b; border-radius: 1rem; padding: 1rem"
diff --git a/config/plugins/visualizations/openlayers/config/openlayers.xml b/config/plugins/visualizations/openlayers/config/openlayers.xml
index 19b89de75375..71c36fb1fe18 100644
--- a/config/plugins/visualizations/openlayers/config/openlayers.xml
+++ b/config/plugins/visualizations/openlayers/config/openlayers.xml
@@ -6,14 +6,17 @@
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
             <test test_attr="ext" result_type="datatype">geojson</test>
-           <test test_attr="ext" result_type="datatype">shp</test>
+            <test test_attr="ext" result_type="datatype">shp</test>
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="ol.css"/>
+    <requirements>
+        <requirement type="npm" version="0.0.2" package="galaxy-openlayers"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
     <settings>
         <input>
             <label>Types of geometry</label>
@@ -21,7 +24,7 @@
             <help>Select a geometry type.</help>
             <type>select</type>
             <display>radio</display>
-            <value>circle</value>
+            <value>Circle</value>
             <data>
                 <data>
                     <label>None</label>
diff --git a/config/plugins/visualizations/openlayers/package.json b/config/plugins/visualizations/openlayers/package.json
deleted file mode 100644
index 17f1cb6c590f..000000000000
--- a/config/plugins/visualizations/openlayers/package.json
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.1.0",
-    "description": "Map visualization using OpenLayers",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "axios": "^0.19.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "file-saver": "^2.0.2",
-        "jquery": "^3.3.1",
-        "jszip": "^3.2.2",
-        "jszip-utils": "^0.1.0",
-        "ol": "^5.3.3",
-        "proj4": "^2.5.0",
-        "shpjs": "^3.4.3",
-        "underscore": "^1.8.3"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static --no-source-maps"
-    },
-    "devDependencies": {
-        "buffer": "^6.0.3",
-        "parcel": "^2.12.0",
-        "process": "^0.11.10",
-        "string_decoder": "^1.3.0"
-    }
-}
diff --git a/config/plugins/visualizations/openlayers/src/script.js b/config/plugins/visualizations/openlayers/src/script.js
deleted file mode 100644
index 90922403fa7f..000000000000
--- a/config/plugins/visualizations/openlayers/src/script.js
+++ /dev/null
@@ -1,260 +0,0 @@
-import $ from "jquery";
-import _ from "underscore";
-
-import { Map, View, Graticule } from "ol";
-import { OSM, Vector } from "ol/source";
-import { GeoJSON } from "ol/format";
-import * as interaction from "ol/interaction";
-import * as style from "ol/style";
-import * as layer from "ol/layer";
-import * as control from "ol/control";
-import { saveAs } from "file-saver";
-
-import shp from "shpjs";
-import axios from "axios";
-
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
-
-var MapViewer = (function(mv) {
-    mv.gMap = null;
-
-    /** Set the style properties of shapes */
-    mv.setStyle = selectedColor => {
-        const styles = {
-            Polygon: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            Circle: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            Point: new style.Style({
-                image: new style.Circle({
-                    radius: 5,
-                    fill: new style.Fill({
-                        color: "rgba(0, 0, 255, 0.1)"
-                    }),
-                    stroke: new style.Stroke({ color: selectedColor, width: 1 })
-                })
-            }),
-            LineString: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                })
-            }),
-            MultiLineString: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                })
-            }),
-            MultiPoint: new style.Style({
-                image: new style.Circle({
-                    radius: 5,
-                    fill: new style.Fill({
-                        color: "rgba(0, 0, 255, 0.1)"
-                    }),
-                    stroke: new style.Stroke({ color: selectedColor, width: 1 })
-                })
-            }),
-            MultiPolygon: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: "rgba(0, 0, 255, 0.1)"
-                })
-            }),
-            GeometryCollection: new style.Style({
-                stroke: new style.Stroke({
-                    color: selectedColor,
-                    width: 1
-                }),
-                fill: new style.Fill({
-                    color: selectedColor
-                }),
-                image: new style.Circle({
-                    radius: 10,
-                    fill: null,
-                    stroke: new style.Stroke({
-                        color: selectedColor
-                    })
-                })
-            })
-        };
-        return styles;
-    };
-
-    /** Set up events and methods for interactions with map view*/
-    mv.setInteractions = (source, options) => {
-        const geometryType = options.chart.settings.get("geometry_type");
-        const geometryColor = options.chart.settings.get("geometry_color");
-        let drawInteraction;
-
-        const addInteraction = () => {
-            if (geometryType !== "None") {
-                drawInteraction = new interaction.Draw({
-                    source: source,
-                    type: geometryType,
-                    freehand: true
-                });
-                drawInteraction.on("drawstart", event => {
-                    const sty = new style.Style({
-                        stroke: new style.Stroke({
-                            color: geometryColor,
-                            width: 2
-                        }),
-                        fill: new style.Fill({
-                            color: "rgba(0, 0, 255, 0.1)"
-                        })
-                    });
-                    event.feature.setStyle(sty);
-                });
-                mv.gMap.addInteraction(drawInteraction);
-            }
-        };
-        addInteraction();
-    };
-
-    /** Export the map view to PNG image*/
-    mv.exportMap = () => {
-        mv.gMap.once("rendercomplete", event => {
-            const canvas = event.context.canvas;
-            let fileName = Math.random()
-                .toString(11)
-                .replace("0.", "");
-            fileName += ".png";
-            if (navigator.msSaveBlob) {
-                navigator.msSaveBlob(canvas.msToBlob(), fileName);
-            } else {
-                canvas.toBlob(blob => {
-                    saveAs(blob, fileName);
-                });
-            }
-        });
-        mv.gMap.renderSync();
-    };
-
-    /** Create the map view */
-    mv.setMap = (vSource, target, options, styleFunction) => {
-        const tile = new layer.Tile({ source: new OSM() });
-        // add fullscreen handle
-        const fullScreen = new control.FullScreen();
-        // add scale to the map
-        const scaleLineControl = new control.ScaleLine();
-        // create vector with styles
-        const vectorLayer = new layer.Vector({
-            source: vSource,
-            style: styleFunction
-        });
-
-        const view = new View({
-            center: [0, 0],
-            zoom: 2
-        });
-
-        // create map view
-        mv.gMap = new Map({
-            controls: control.defaults().extend([scaleLineControl, fullScreen]),
-            interactions: interaction.defaults().extend([new interaction.DragRotateAndZoom()]),
-            layers: [tile, vectorLayer],
-            target: target,
-            loadTilesWhileInteracting: true,
-            view: view
-        });
-
-        // add grid lines
-        const graticule = new Graticule({
-            strokeStyle: new style.Stroke({
-                color: "rgba(255, 120, 0, 0.9)",
-                width: 2,
-                lineDash: [0.5, 4]
-            }),
-            showLabels: true
-        });
-
-        mv.gMap.addInteraction(new interaction.Modify({ source: vSource }));
-        mv.gMap.addControl(new control.ZoomSlider());
-        graticule.setMap(mv.gMap);
-        mv.setInteractions(vSource, options);
-    };
-
-    /** Load the map GeoJson and Shapefiles*/
-    mv.loadFile = (filePath, fileType, options, chart) => {
-        const target = options.target;
-        const formatType = new GeoJSON();
-        const toExport = options.chart.settings.get("export_map");
-        const geometryColor = options.chart.settings.get("geometry_color");
-        const selectedStyles = mv.setStyle(geometryColor);
-        const styleFunction = feature => {
-            return selectedStyles[feature.getGeometry().getType()];
-        };
-
-        if (toExport === "export") {
-            mv.exportMap();
-        }
-
-        if (fileType === "geojson") {
-            const sourceVec = new Vector({ format: formatType, url: filePath, wrapX: false });
-            mv.createMap(filePath, sourceVec, options, chart, styleFunction, target);
-        } else if (fileType === "shp") {
-            axios.get(filePath, { responseType: "arraybuffer" }).then(shpfile => {
-                console.debug(shpfile);
-                shp(shpfile.data).then(
-                    geojson => {
-                        const url = window.URL.createObjectURL(
-                            new Blob([JSON.stringify(geojson)], { type: "application/json" })
-                        );
-                        const sourceVec = new Vector({ format: formatType, url: url, wrapX: false });
-                        mv.createMap(url, sourceVec, options, chart, styleFunction, target);
-                    },
-                    failure => {
-                        console.debug("FAILURE!", failure);
-                    }
-                );
-            });
-        }
-    };
-
-    mv.createMap = (filePath, sourceVec, options, chart, styleFunction, target) => {
-        mv.setMap(sourceVec, target, options, styleFunction);
-        chart.state("ok", "Chart drawn.");
-        options.process.resolve();
-    };
-
-    return mv;
-})(MapViewer || {});
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    const chart = options.chart;
-    const dataset = options.dataset;
-    const downloadUrl = prefixedDownloadUrl(options.root, dataset.download_url);
-    $.ajax({
-        url: downloadUrl,
-        success: () => {
-            MapViewer.loadFile(downloadUrl, dataset.extension, options, chart);
-        },
-        error: () => {
-            chart.state("failed", "Failed to access dataset.");
-            options.process.resolve();
-        }
-    });
-}
diff --git a/config/plugins/visualizations/openlayers/static/logo.png b/config/plugins/visualizations/openlayers/static/logo.png
deleted file mode 100644
index 29a440ff2bdb..000000000000
Binary files a/config/plugins/visualizations/openlayers/static/logo.png and /dev/null differ
diff --git a/config/plugins/visualizations/openlayers/static/logo.svg b/config/plugins/visualizations/openlayers/static/logo.svg
new file mode 100644
index 000000000000..6295e16b8a35
--- /dev/null
+++ b/config/plugins/visualizations/openlayers/static/logo.svg
@@ -0,0 +1 @@
+<svg width="2471" height="2500" viewBox="0 0 256 259" xmlns="http://www.w3.org/2000/svg" preserveAspectRatio="xMinYMin meet"><path d="M94.029 57.213c18.682-15.559 49.26-15.562 67.945 0l80.016 66.632c18.68 15.561 18.683 41.015-.003 56.577l-80.013 66.63c-18.69 15.564-49.266 15.56-67.945 0l-80.016-66.63c-18.683-15.56-18.683-41.016-.003-56.577l80.019-66.632z" fill="#015965"/><path d="M94.029 35.561c18.682-15.559 49.26-15.562 67.945 0l80.016 66.633c18.68 15.562 18.683 41.017-.003 56.578l-80.013 66.63c-18.69 15.564-49.266 15.56-67.945 0l-80.016-66.63c-18.683-15.56-18.683-41.016-.003-56.578L94.029 35.56z" fill="#E5E5E5"/><path d="M161.974 12.319L241.99 78.95c18.68 15.562 18.683 41.017-.003 56.578l-80.013 66.63c-18.69 15.565-49.266 15.56-67.945 0l-80.016-66.63C-4.67 119.97-4.67 94.513 14.01 78.951l80.019-66.632c18.682-15.56 49.26-15.563 67.945 0z" fill="#35BBCE"/><path d="M244.31 81.1a42.693 42.693 0 0 0-2.3-2.077L161.99 12.33c-18.688-15.577-49.267-15.574-67.952 0L14.011 79.023c-18.681 15.58-18.681 41.058.003 56.634l8.612 7.176C45.142 115.79 121.074 40.853 244.31 81.1z" opacity=".15" fill="#FFF"/></svg>
\ No newline at end of file
diff --git a/config/plugins/visualizations/openlayers/static/ol.css b/config/plugins/visualizations/openlayers/static/ol.css
deleted file mode 100644
index 79d87d00a509..000000000000
--- a/config/plugins/visualizations/openlayers/static/ol.css
+++ /dev/null
@@ -1,251 +0,0 @@
-.ol-box {
-  box-sizing: border-box;
-  border-radius: 2px;
-  border: 2px solid blue;
-}
-
-.ol-mouse-position {
-  top: 8px;
-  right: 8px;
-  position: absolute;
-}
-
-.ol-scale-line {
-  background: rgba(0,60,136,0.3);
-  border-radius: 4px;
-  bottom: 8px;
-  left: 8px;
-  padding: 2px;
-  position: absolute;
-}
-.ol-scale-line-inner {
-  border: 1px solid #eee;
-  border-top: none;
-  color: #eee;
-  font-size: 10px;
-  text-align: center;
-  margin: 1px;
-  will-change: contents, width;
-}
-.ol-overlay-container {
-  will-change: left,right,top,bottom;
-}
-
-.ol-unsupported {
-  display: none;
-}
-.ol-viewport, .ol-unselectable {
-  -webkit-touch-callout: none;
-  -webkit-user-select: none;
-  -moz-user-select: none;
-  -ms-user-select: none;
-  user-select: none;
-  -webkit-tap-highlight-color: rgba(0,0,0,0);
-}
-.ol-selectable {
-  -webkit-touch-callout: default;
-  -webkit-user-select: text;
-  -moz-user-select: text;
-  -ms-user-select: text;
-  user-select: text;
-}
-.ol-grabbing {
-  cursor: -webkit-grabbing;
-  cursor: -moz-grabbing;
-  cursor: grabbing;
-}
-.ol-grab {
-  cursor: move;
-  cursor: -webkit-grab;
-  cursor: -moz-grab;
-  cursor: grab;
-}
-.ol-control {
-  position: absolute;
-  background-color: rgba(255,255,255,0.4);
-  border-radius: 4px;
-  padding: 2px;
-}
-.ol-control:hover {
-  background-color: rgba(255,255,255,0.6);
-}
-.ol-zoom {
-  top: .5em;
-  left: .5em;
-}
-.ol-rotate {
-  top: .5em;
-  right: .5em;
-  transition: opacity .25s linear, visibility 0s linear;
-}
-.ol-rotate.ol-hidden {
-  opacity: 0;
-  visibility: hidden;
-  transition: opacity .25s linear, visibility 0s linear .25s;
-}
-.ol-zoom-extent {
-  top: 4.643em;
-  left: .5em;
-}
-.ol-full-screen {
-  right: .5em;
-  top: .5em;
-}
-@media print {
-  .ol-control {
-    display: none;
-  }
-}
-
-.ol-control button {
-  display: block;
-  margin: 1px;
-  padding: 0;
-  color: white;
-  font-size: 1.14em;
-  font-weight: bold;
-  text-decoration: none;
-  text-align: center;
-  height: 1.375em;
-  width: 1.375em;
-  line-height: .4em;
-  background-color: rgba(0,60,136,0.5);
-  border: none;
-  border-radius: 2px;
-}
-.ol-control button::-moz-focus-inner {
-  border: none;
-  padding: 0;
-}
-.ol-zoom-extent button {
-  line-height: 1.4em;
-}
-.ol-compass {
-  display: block;
-  font-weight: normal;
-  font-size: 1.2em;
-  will-change: transform;
-}
-.ol-touch .ol-control button {
-  font-size: 1.5em;
-}
-.ol-touch .ol-zoom-extent {
-  top: 5.5em;
-}
-.ol-control button:hover,
-.ol-control button:focus {
-  text-decoration: none;
-  background-color: rgba(0,60,136,0.7);
-}
-.ol-zoom .ol-zoom-in {
-  border-radius: 2px 2px 0 0;
-}
-.ol-zoom .ol-zoom-out {
-  border-radius: 0 0 2px 2px;
-}
-
-
-.ol-attribution {
-  text-align: right;
-  bottom: .5em;
-  right: .5em;
-  max-width: calc(100% - 1.3em);
-}
-
-.ol-attribution ul {
-  margin: 0;
-  padding: 0 .5em;
-  font-size: .7rem;
-  line-height: 1.375em;
-  color: #000;
-  text-shadow: 0 0 2px #fff;
-}
-.ol-attribution li {
-  display: inline;
-  list-style: none;
-  line-height: inherit;
-}
-.ol-attribution li:not(:last-child):after {
-  content: " ";
-}
-.ol-attribution img {
-  max-height: 2em;
-  max-width: inherit;
-  vertical-align: middle;
-}
-.ol-attribution ul, .ol-attribution button {
-  display: inline-block;
-}
-.ol-attribution.ol-collapsed ul {
-  display: none;
-}
-.ol-attribution:not(.ol-collapsed) {
-  background: rgba(255,255,255,0.8);
-}
-.ol-attribution.ol-uncollapsible {
-  bottom: 0;
-  right: 0;
-  border-radius: 4px 0 0;
-  height: 1.1em;
-  line-height: 1em;
-}
-.ol-attribution.ol-uncollapsible img {
-  margin-top: -.2em;
-  max-height: 1.6em;
-}
-.ol-attribution.ol-uncollapsible button {
-  display: none;
-}
-
-.ol-zoomslider {
-  top: 4.5em;
-  left: .5em;
-  height: 200px;
-}
-.ol-zoomslider button {
-  position: relative;
-  height: 10px;
-}
-
-.ol-touch .ol-zoomslider {
-  top: 5.5em;
-}
-
-.ol-overviewmap {
-  left: 0.5em;
-  bottom: 0.5em;
-}
-.ol-overviewmap.ol-uncollapsible {
-  bottom: 0;
-  left: 0;
-  border-radius: 0 4px 0 0;
-}
-.ol-overviewmap .ol-overviewmap-map,
-.ol-overviewmap button {
-  display: inline-block;
-}
-.ol-overviewmap .ol-overviewmap-map {
-  border: 1px solid #7b98bc;
-  height: 150px;
-  margin: 2px;
-  width: 150px;
-}
-.ol-overviewmap:not(.ol-collapsed) button{
-  bottom: 1px;
-  left: 2px;
-  position: absolute;
-}
-.ol-overviewmap.ol-collapsed .ol-overviewmap-map,
-.ol-overviewmap.ol-uncollapsible button {
-  display: none;
-}
-.ol-overviewmap:not(.ol-collapsed) {
-  background: rgba(255,255,255,0.8);
-}
-.ol-overviewmap-box {
-  border: 2px dotted rgba(0,60,136,0.7);
-}
-
-.ol-overviewmap .ol-overviewmap-box:hover {
-  cursor: move;
-}
diff --git a/config/plugins/visualizations/phylocanvas/package.json b/config/plugins/visualizations/phylocanvas/package.json
index 24d6e23f0fb5..efee4654d8d6 100644
--- a/config/plugins/visualizations/phylocanvas/package.json
+++ b/config/plugins/visualizations/phylocanvas/package.json
@@ -15,6 +15,7 @@
         "build": "parcel build src/script.js --dist-dir static"
     },
     "devDependencies": {
+        "buffer": "^6.0.3",
         "parcel": "^2.12.0",
         "process": "^0.11.10"
     }
diff --git a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
index 99763daa554f..84d14366f62c 100644
--- a/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
+++ b/config/plugins/visualizations/tiffviewer/config/tiffviewer.xml
@@ -1,18 +1,16 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
 <visualization name="Tiff Viewer">
-    <description>Basic Tiff Image visualization</description>
+    <description>Tiff Image Viewer</description>
     <data_sources>
         <data_source>
             <model_class>HistoryDatasetAssociation</model_class>
-
             <test type="isinstance" test_attr="datatype" result_type="datatype">images.Tiff</test>
-
             <to_param param_attr="id">dataset_id</to_param>
         </data_source>
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="script.css"/>
+    <entry_point entry_point_type="script" src="script.js" css="script.css"/>
 </visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/tiffviewer/src/script.js b/config/plugins/visualizations/tiffviewer/src/script.js
index a16a82253d1a..f97bf19d255a 100644
--- a/config/plugins/visualizations/tiffviewer/src/script.js
+++ b/config/plugins/visualizations/tiffviewer/src/script.js
@@ -8,22 +8,15 @@ const App = (props) => {
     return <TIFFViewer tiff={props.dataset_url} paginate="bottom" />;
 };
 
-/* This will be part of the charts/viz standard lib in 23.1 */
-const slashCleanup = /(\/)+/g;
-function prefixedDownloadUrl(root, path) {
-    return `${root}/${path}`.replace(slashCleanup, "/");
-}
+const { root, visualization_config } = JSON.parse(document.getElementById("app").dataset.incoming);
 
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    const dataset = options.dataset;
-    const url = prefixedDownloadUrl(options.root, dataset.download_url);
-    const root = createRoot(document.getElementById(options.target));
-    root.render(
-        <StrictMode>
-            <App dataset_url={url} />
-        </StrictMode>
-    );
-    options.chart.state("ok", "Done.");
-    options.process.resolve();
-};
+const datasetId = visualization_config.dataset_id;
+
+const url = window.location.origin + root + "api/datasets/" + datasetId + "/display";
+
+const rootElement = createRoot(document.getElementById("app"));
+rootElement.render(
+    <StrictMode>
+        <App dataset_url={url} />
+    </StrictMode>
+);
diff --git a/config/plugins/visualizations/venn/config/venn.xml b/config/plugins/visualizations/venn/config/venn.xml
index a46fa31a9aa0..25e140440fa3 100644
--- a/config/plugins/visualizations/venn/config/venn.xml
+++ b/config/plugins/visualizations/venn/config/venn.xml
@@ -13,8 +13,11 @@
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
     </params>
-    <entry_point entry_point_type="chart" src="script.js" css="script.css"/>
-    <groups>
+    <requirements>
+        <requirement type="npm" version="0.0.2" package="@galaxyproject/venn"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <tracks>
         <input>
             <label>Provide a label</label>
             <name>key</name>
@@ -28,5 +31,5 @@
             <type>data_column</type>
             <is_label>true</is_label>
         </input>
-    </groups>
+    </tracks>
 </visualization>
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/package.json b/config/plugins/visualizations/venn/package.json
deleted file mode 100644
index 2ed9970cabb5..000000000000
--- a/config/plugins/visualizations/venn/package.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
-    "name": "visualization",
-    "version": "0.2.0",
-    "keywords": [
-        "galaxy",
-        "visualization"
-    ],
-    "license": "AFL-3.0",
-    "dependencies": {
-        "@galaxyproject/charts": "^0.1.0",
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
-        "bootstrap": "^3.3.7",
-        "d3": "^3.4.5",
-        "jquery": "^3.1.1",
-        "underscore": "^1.13.1"
-    },
-    "scripts": {
-        "build": "parcel build src/script.js --dist-dir static"
-    },
-    "devDependencies": {
-        "parcel": "2.11.0"
-    }
-}
diff --git a/config/plugins/visualizations/venn/src/script.js b/config/plugins/visualizations/venn/src/script.js
deleted file mode 100644
index bd24659752c1..000000000000
--- a/config/plugins/visualizations/venn/src/script.js
+++ /dev/null
@@ -1,93 +0,0 @@
-import * as Venn from "./venn";
-import * as d3 from "d3";
-import _ from "underscore";
-window.d3 = d3;
-import { request as requestDatasets } from "@galaxyproject/charts/lib/utilities/datasets";
-
-function _combinations( current, remaining, results ) {
-    _.each( remaining, function( value, index ) {
-        var new_current = current.slice();
-        var new_remaining = remaining.slice();
-        new_remaining.splice( 0, index + 1 );
-        new_current.push( value );
-        results.push( new_current );
-        _combinations( new_current, new_remaining, results );
-    });
-};
-
-window.bundleEntries = window.bundleEntries || {};
-window.bundleEntries.load = function (options) {
-    requestDatasets({
-        root            : options.root,
-        chart           : options.chart,
-        dataset_id      : options.chart.get( 'dataset_id' ),
-        dataset_groups  : options.chart.groups,
-        success         : function( result ) {
-            var group_keys   = [];
-            var group_values = [];
-            var all_values   = {};
-            var set_size     = {};
-            var group_ids    = [];
-            _.each( result, function( group, i ) {
-                var group_index = {};
-                _.each( group.values, function( d ) {
-                    all_values[ d.observation ] = group_index[ d.observation ] = true;
-                });
-                group_keys.push( group.key );
-                group_values.push( group_index );
-                group_ids.push( i );
-            });
-            var combos = [];
-            _combinations( [], group_ids, combos );
-            var sets = [];
-            _.each( combos, function( c ) {
-                var size = 0;
-                for ( var value in all_values ) {
-                    var found = 0;
-                    _.each( c, function( group_id ) {
-                        if ( group_values[ group_id ][ value ] ) {
-                            found++;
-                        }
-                    });
-                    if ( found == c.length ) {
-                        size++;
-                    }
-                }
-                if ( size > 0 ) {
-                    var set_labels = [];
-                    _.each( c, function( id ) {
-                        set_labels.push( group_keys[ id ]);
-                    });
-                    sets.push( { sets: set_labels, size: size } );
-                }
-            });
-            $('#' + options.target).append("<svg/>")
-                                   .attr("id", "svg-" + options.target)
-                                   .css("height", "100%")
-                                   .css("width", "100%");
-            var svg = d3.select( '#svg-' + options.target ).datum( sets ).call( Venn.VennDiagram() );
-            var tooltip = null;
-            svg.selectAll( 'g' )
-                .on( 'mouseover', function( d, i ) {
-                    Venn.sortAreas( svg, d );
-                    tooltip = d3.select( 'body' ).append( 'div' ).attr( 'class', 'venntooltip' );
-                    tooltip.transition().duration( 400 ).style( 'opacity', .9 );
-                    tooltip.text(d.size );
-                    var selection = d3.select( this ).transition( 'tooltip' ).duration( 400 );
-                    selection.select( 'path' )
-                                .style( 'stroke-width', 3 )
-                                .style( 'fill-opacity', d.sets.length == 1 ? .4 : .1 )
-                                .style( 'stroke-opacity', 1 );
-                })
-                .on( 'mousemove', function() {
-                    tooltip.style( 'left', ( d3.event.pageX ) + 'px')
-                            .style( 'top', ( d3.event.pageY - 28 ) + 'px');
-                })
-                .on( 'mouseout', function( d, i ) {
-                    tooltip.remove();
-                });
-            options.chart.state( 'ok', 'Venn diagram drawn.' );
-            options.process.resolve();
-        }
-    });
-}
diff --git a/config/plugins/visualizations/venn/src/venn.js b/config/plugins/visualizations/venn/src/venn.js
deleted file mode 100644
index 58a29e784b3f..000000000000
--- a/config/plugins/visualizations/venn/src/venn.js
+++ /dev/null
@@ -1,1789 +0,0 @@
-(function (global, factory) {
-    typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) :
-    typeof define === 'function' && define.amd ? define(['exports'], factory) :
-    factory((global.venn = {}),global.d3,global.d3);
-}(this, function (exports) { 'use strict';
-
-    /** finds the zeros of a function, given two starting points (which must
-     * have opposite signs */
-    function bisect(f, a, b, parameters) {
-        parameters = parameters || {};
-        var maxIterations = parameters.maxIterations || 100,
-            tolerance = parameters.tolerance || 1e-10,
-            fA = f(a),
-            fB = f(b),
-            delta = b - a;
-
-        if (fA * fB > 0) {
-            throw "Initial bisect points must have opposite signs";
-        }
-
-        if (fA === 0) return a;
-        if (fB === 0) return b;
-
-        for (var i = 0; i < maxIterations; ++i) {
-            delta /= 2;
-            var mid = a + delta,
-                fMid = f(mid);
-
-            if (fMid * fA >= 0) {
-                a = mid;
-            }
-
-            if ((Math.abs(delta) < tolerance) || (fMid === 0)) {
-                return mid;
-            }
-        }
-        return a + delta;
-    }
-
-    // need some basic operations on vectors, rather than adding a dependency,
-    // just define here
-    function zeros(x) { var r = new Array(x); for (var i = 0; i < x; ++i) { r[i] = 0; } return r; }
-    function zerosM(x,y) { return zeros(x).map(function() { return zeros(y); }); }
-
-    function dot(a, b) {
-        var ret = 0;
-        for (var i = 0; i < a.length; ++i) {
-            ret += a[i] * b[i];
-        }
-        return ret;
-    }
-
-    function norm2(a)  {
-        return Math.sqrt(dot(a, a));
-    }
-
-    function multiplyBy(a, c) {
-        for (var i = 0; i < a.length; ++i) {
-            a[i] *= c;
-        }
-    }
-
-    function weightedSum(ret, w1, v1, w2, v2) {
-        for (var j = 0; j < ret.length; ++j) {
-            ret[j] = w1 * v1[j] + w2 * v2[j];
-        }
-    }
-
-    /** minimizes a function using the downhill simplex method */
-    function fmin(f, x0, parameters) {
-        parameters = parameters || {};
-
-        var maxIterations = parameters.maxIterations || x0.length * 200,
-            nonZeroDelta = parameters.nonZeroDelta || 1.1,
-            zeroDelta = parameters.zeroDelta || 0.001,
-            minErrorDelta = parameters.minErrorDelta || 1e-6,
-            minTolerance = parameters.minErrorDelta || 1e-5,
-            rho = parameters.rho || 1,
-            chi = parameters.chi || 2,
-            psi = parameters.psi || -0.5,
-            sigma = parameters.sigma || 0.5,
-            callback = parameters.callback,
-            maxDiff,
-            temp;
-
-        // initialize simplex.
-        var N = x0.length,
-            simplex = new Array(N + 1);
-        simplex[0] = x0;
-        simplex[0].fx = f(x0);
-        for (var i = 0; i < N; ++i) {
-            var point = x0.slice();
-            point[i] = point[i] ? point[i] * nonZeroDelta : zeroDelta;
-            simplex[i+1] = point;
-            simplex[i+1].fx = f(point);
-        }
-
-        var sortOrder = function(a, b) { return a.fx - b.fx; };
-
-        var centroid = x0.slice(),
-            reflected = x0.slice(),
-            contracted = x0.slice(),
-            expanded = x0.slice();
-
-        for (var iteration = 0; iteration < maxIterations; ++iteration) {
-            simplex.sort(sortOrder);
-            if (callback) {
-                callback(simplex);
-            }
-
-            maxDiff = 0;
-            for (i = 0; i < N; ++i) {
-                maxDiff = Math.max(maxDiff, Math.abs(simplex[0][i] - simplex[1][i]));
-            }
-
-            if ((Math.abs(simplex[0].fx - simplex[N].fx) < minErrorDelta) &&
-                (maxDiff < minTolerance)) {
-                break;
-            }
-
-            // compute the centroid of all but the worst point in the simplex
-            for (i = 0; i < N; ++i) {
-                centroid[i] = 0;
-                for (var j = 0; j < N; ++j) {
-                    centroid[i] += simplex[j][i];
-                }
-                centroid[i] /= N;
-            }
-
-            // reflect the worst point past the centroid  and compute loss at reflected
-            // point
-            var worst = simplex[N];
-            weightedSum(reflected, 1+rho, centroid, -rho, worst);
-            reflected.fx = f(reflected);
-
-            // if the reflected point is the best seen, then possibly expand
-            if (reflected.fx <= simplex[0].fx) {
-                weightedSum(expanded, 1+chi, centroid, -chi, worst);
-                expanded.fx = f(expanded);
-                if (expanded.fx < reflected.fx) {
-                    temp = simplex[N];
-                    simplex[N] = expanded;
-                    expanded = temp;
-                }  else {
-                    temp = simplex[N];
-                    simplex[N] = reflected;
-                    reflected = temp;
-                }
-            }
-
-            // if the reflected point is worse than the second worst, we need to
-            // contract
-            else if (reflected.fx >= simplex[N-1].fx) {
-                var shouldReduce = false;
-
-                if (reflected.fx > worst.fx) {
-                    // do an inside contraction
-                    weightedSum(contracted, 1+psi, centroid, -psi, worst);
-                    contracted.fx = f(contracted);
-                    if (contracted.fx < worst.fx) {
-                        temp = simplex[N];
-                        simplex[N] = contracted;
-                        contracted = temp;
-                    } else {
-                        shouldReduce = true;
-                    }
-                } else {
-                    // do an outside contraction
-                    weightedSum(contracted, 1-psi * rho, centroid, psi*rho, worst);
-                    contracted.fx = f(contracted);
-                    if (contracted.fx <= reflected.fx) {
-                        temp = simplex[N];
-                        simplex[N] = contracted;
-                        contracted = temp;
-                    } else {
-                        shouldReduce = true;
-                    }
-                }
-
-                if (shouldReduce) {
-                    // do reduction. doesn't actually happen that often
-                    for (i = 1; i < simplex.length; ++i) {
-                        weightedSum(simplex[i], 1 - sigma, simplex[0], sigma, simplex[i]);
-                        simplex[i].fx = f(simplex[i]);
-                    }
-                }
-            } else {
-                temp = simplex[N];
-                simplex[N] = reflected;
-                reflected = temp;
-            }
-
-        }
-
-        simplex.sort(sortOrder);
-        return {f : simplex[0].fx,
-                solution : simplex[0]};
-    }
-
-    function minimizeConjugateGradient(f, initial, params) {
-        // allocate all memory up front here, keep out of the loop for perfomance
-        // reasons
-        var current = {x: initial.slice(), fx: 0, fxprime: initial.slice()},
-            next = {x: initial.slice(), fx: 0, fxprime: initial.slice()},
-            yk = initial.slice(),
-            pk, temp,
-            a = 1,
-            maxIterations;
-
-        params = params || {};
-        maxIterations = params.maxIterations || initial.length * 5;
-
-        current.fx = f(current.x, current.fxprime);
-        pk = current.fxprime.slice();
-        multiplyBy(pk, -1);
-
-        for (var i = 0; i < maxIterations; ++i) {
-            if (params.history) {
-                params.history.push({x: current.x.slice(),
-                                     fx: current.fx,
-                                     fxprime: current.fxprime.slice()});
-            }
-
-            a = wolfeLineSearch(f, pk, current, next, a);
-            if (!a) {
-                // faiiled to find point that satifies wolfe conditions.
-                // reset direction for next iteration
-                for (var j = 0; j < pk.length; ++j) {
-                    pk[j] = -1 * current.fxprime[j];
-                }
-            } else {
-                // update direction using Polak–Ribiere CG method
-                weightedSum(yk, 1, next.fxprime, -1, current.fxprime);
-
-                var delta_k = dot(current.fxprime, current.fxprime),
-                    beta_k = Math.max(0, dot(yk, next.fxprime) / delta_k);
-
-                weightedSum(pk, beta_k, pk, -1, next.fxprime);
-
-                temp = current;
-                current = next;
-                next = temp;
-            }
-
-            if (norm2(current.fxprime) <= 1e-5) {
-                break;
-            }
-        }
-
-        if (params.history) {
-            params.history.push({x: current.x.slice(),
-                                 fx: current.fx,
-                                 fxprime: current.fxprime.slice()});
-        }
-
-        return current;
-    }
-
-    var c1 = 1e-6;
-    var c2 = 0.1;
-    /// searches along line 'pk' for a point that satifies the wolfe conditions
-    /// See 'Numerical Optimization' by Nocedal and Wright p59-60
-    function wolfeLineSearch(f, pk, current, next, a) {
-        var phi0 = current.fx, phiPrime0 = dot(current.fxprime, pk),
-            phi = phi0, phi_old = phi0,
-            phiPrime = phiPrime0,
-            a0 = 0;
-
-        a = a || 1;
-
-        function zoom(a_lo, a_high, phi_lo) {
-            for (var iteration = 0; iteration < 16; ++iteration) {
-                a = (a_lo + a_high)/2;
-                weightedSum(next.x, 1.0, current.x, a, pk);
-                phi = next.fx = f(next.x, next.fxprime);
-                phiPrime = dot(next.fxprime, pk);
-
-                if ((phi > (phi0 + c1 * a * phiPrime0)) ||
-                    (phi >= phi_lo)) {
-                    a_high = a;
-
-                } else  {
-                    if (Math.abs(phiPrime) <= -c2 * phiPrime0) {
-                        return a;
-                    }
-
-                    if (phiPrime * (a_high - a_lo) >=0) {
-                        a_high = a_lo;
-                    }
-
-                    a_lo = a;
-                    phi_lo = phi;
-                }
-            }
-
-            return 0;
-        }
-
-        for (var iteration = 0; iteration < 10; ++iteration) {
-            weightedSum(next.x, 1.0, current.x, a, pk);
-            phi = next.fx = f(next.x, next.fxprime);
-            phiPrime = dot(next.fxprime, pk);
-            if ((phi > (phi0 + c1 * a * phiPrime0)) ||
-                (iteration && (phi >= phi_old))) {
-                return zoom(a0, a, phi_old);
-            }
-
-            if (Math.abs(phiPrime) <= -c2 * phiPrime0) {
-                return a;
-            }
-
-            if (phiPrime >= 0 ) {
-                return zoom(a, a0, phi);
-            }
-
-            phi_old = phi;
-            a0 = a;
-            a *= 2;
-        }
-
-        return 0;
-    }
-
-    var SMALL = 1e-10;
-
-    /** Returns the intersection area of a bunch of circles (where each circle
-     is an object having an x,y and radius property) */
-    function intersectionArea(circles, stats) {
-        // get all the intersection points of the circles
-        var intersectionPoints = getIntersectionPoints(circles);
-
-        // filter out points that aren't included in all the circles
-        var innerPoints = intersectionPoints.filter(function (p) {
-            return containedInCircles(p, circles);
-        });
-
-        var arcArea = 0, polygonArea = 0, arcs = [], i;
-
-        // if we have intersection points that are within all the circles,
-        // then figure out the area contained by them
-        if (innerPoints.length > 1) {
-            // sort the points by angle from the center of the polygon, which lets
-            // us just iterate over points to get the edges
-            var center = getCenter(innerPoints);
-            for (i = 0; i < innerPoints.length; ++i ) {
-                var p = innerPoints[i];
-                p.angle = Math.atan2(p.x - center.x, p.y - center.y);
-            }
-            innerPoints.sort(function(a,b) { return b.angle - a.angle;});
-
-            // iterate over all points, get arc between the points
-            // and update the areas
-            var p2 = innerPoints[innerPoints.length - 1];
-            for (i = 0; i < innerPoints.length; ++i) {
-                var p1 = innerPoints[i];
-
-                // polygon area updates easily ...
-                polygonArea += (p2.x + p1.x) * (p1.y - p2.y);
-
-                // updating the arc area is a little more involved
-                var midPoint = {x : (p1.x + p2.x) / 2,
-                                y : (p1.y + p2.y) / 2},
-                    arc = null;
-
-                for (var j = 0; j < p1.parentIndex.length; ++j) {
-                    if (p2.parentIndex.indexOf(p1.parentIndex[j]) > -1) {
-                        // figure out the angle halfway between the two points
-                        // on the current circle
-                        var circle = circles[p1.parentIndex[j]],
-                            a1 = Math.atan2(p1.x - circle.x, p1.y - circle.y),
-                            a2 = Math.atan2(p2.x - circle.x, p2.y - circle.y);
-
-                        var angleDiff = (a2 - a1);
-                        if (angleDiff < 0) {
-                            angleDiff += 2*Math.PI;
-                        }
-
-                        // and use that angle to figure out the width of the
-                        // arc
-                        var a = a2 - angleDiff/2,
-                            width = distance(midPoint, {
-                                x : circle.x + circle.radius * Math.sin(a),
-                                y : circle.y + circle.radius * Math.cos(a)
-                            });
-
-                        // pick the circle whose arc has the smallest width
-                        if ((arc === null) || (arc.width > width)) {
-                            arc = { circle : circle,
-                                    width : width,
-                                    p1 : p1,
-                                    p2 : p2};
-                        }
-                    }
-                }
-
-                if (arc !== null) {
-                    arcs.push(arc);
-                    arcArea += circleArea(arc.circle.radius, arc.width);
-                    p2 = p1;
-                }
-            }
-        } else {
-            // no intersection points, is either disjoint - or is completely
-            // overlapped. figure out which by examining the smallest circle
-            var smallest = circles[0];
-            for (i = 1; i < circles.length; ++i) {
-                if (circles[i].radius < smallest.radius) {
-                    smallest = circles[i];
-                }
-            }
-
-            // make sure the smallest circle is completely contained in all
-            // the other circles
-            var disjoint = false;
-            for (i = 0; i < circles.length; ++i) {
-                if (distance(circles[i], smallest) > Math.abs(smallest.radius - circles[i].radius)) {
-                    disjoint = true;
-                    break;
-                }
-            }
-
-            if (disjoint) {
-                arcArea = polygonArea = 0;
-
-            } else {
-                arcArea = smallest.radius * smallest.radius * Math.PI;
-                arcs.push({circle : smallest,
-                           p1: { x: smallest.x,        y : smallest.y + smallest.radius},
-                           p2: { x: smallest.x - SMALL, y : smallest.y + smallest.radius},
-                           width : smallest.radius * 2 });
-            }
-        }
-
-        polygonArea /= 2;
-        if (stats) {
-            stats.area = arcArea + polygonArea;
-            stats.arcArea = arcArea;
-            stats.polygonArea = polygonArea;
-            stats.arcs = arcs;
-            stats.innerPoints = innerPoints;
-            stats.intersectionPoints = intersectionPoints;
-        }
-
-        return arcArea + polygonArea;
-    }
-
-    /** returns whether a point is contained by all of a list of circles */
-    function containedInCircles(point, circles) {
-        for (var i = 0; i < circles.length; ++i) {
-            if (distance(point, circles[i]) > circles[i].radius + SMALL) {
-                return false;
-            }
-        }
-        return true;
-    }
-
-    /** Gets all intersection points between a bunch of circles */
-    function getIntersectionPoints(circles) {
-        var ret = [];
-        for (var i = 0; i < circles.length; ++i) {
-            for (var j = i + 1; j < circles.length; ++j) {
-                var intersect = circleCircleIntersection(circles[i],
-                                                              circles[j]);
-                for (var k = 0; k < intersect.length; ++k) {
-                    var p = intersect[k];
-                    p.parentIndex = [i,j];
-                    ret.push(p);
-                }
-            }
-        }
-        return ret;
-    }
-
-    function circleIntegral(r, x) {
-        var y = Math.sqrt(r * r - x * x);
-        return x * y + r * r * Math.atan2(x, y);
-    }
-
-    /** Returns the area of a circle of radius r - up to width */
-    function circleArea(r, width) {
-        return circleIntegral(r, width - r) - circleIntegral(r, -r);
-    }
-
-    /** euclidean distance between two points */
-    function distance(p1, p2) {
-        return Math.sqrt((p1.x - p2.x) * (p1.x - p2.x) +
-                         (p1.y - p2.y) * (p1.y - p2.y));
-    }
-
-
-    /** Returns the overlap area of two circles of radius r1 and r2 - that
-    have their centers separated by distance d. Simpler faster
-    circle intersection for only two circles */
-    function circleOverlap(r1, r2, d) {
-        // no overlap
-        if (d >= r1 + r2) {
-            return 0;
-        }
-
-        // completely overlapped
-        if (d <= Math.abs(r1 - r2)) {
-            return Math.PI * Math.min(r1, r2) * Math.min(r1, r2);
-        }
-
-        var w1 = r1 - (d * d - r2 * r2 + r1 * r1) / (2 * d),
-            w2 = r2 - (d * d - r1 * r1 + r2 * r2) / (2 * d);
-        return circleArea(r1, w1) + circleArea(r2, w2);
-    }
-
-    /** Given two circles (containing a x/y/radius attributes),
-    returns the intersecting points if possible.
-    note: doesn't handle cases where there are infinitely many
-    intersection points (circles are equivalent):, or only one intersection point*/
-    function circleCircleIntersection(p1, p2) {
-        var d = distance(p1, p2),
-            r1 = p1.radius,
-            r2 = p2.radius;
-
-        // if to far away, or self contained - can't be done
-        if ((d >= (r1 + r2)) || (d <= Math.abs(r1 - r2))) {
-            return [];
-        }
-
-        var a = (r1 * r1 - r2 * r2 + d * d) / (2 * d),
-            h = Math.sqrt(r1 * r1 - a * a),
-            x0 = p1.x + a * (p2.x - p1.x) / d,
-            y0 = p1.y + a * (p2.y - p1.y) / d,
-            rx = -(p2.y - p1.y) * (h / d),
-            ry = -(p2.x - p1.x) * (h / d);
-
-        return [{x: x0 + rx, y : y0 - ry },
-                {x: x0 - rx, y : y0 + ry }];
-    }
-
-    /** Returns the center of a bunch of points */
-    function getCenter(points) {
-        var center = {x: 0, y: 0};
-        for (var i =0; i < points.length; ++i ) {
-            center.x += points[i].x;
-            center.y += points[i].y;
-        }
-        center.x /= points.length;
-        center.y /= points.length;
-        return center;
-    }
-
-    /** given a list of set objects, and their corresponding overlaps.
-    updates the (x, y, radius) attribute on each set such that their positions
-    roughly correspond to the desired overlaps */
-    function venn(areas, parameters) {
-        parameters = parameters || {};
-        parameters.maxIterations = parameters.maxIterations || 500;
-        var initialLayout = parameters.initialLayout || bestInitialLayout;
-
-        // add in missing pairwise areas as having 0 size
-        areas = addMissingAreas(areas);
-
-        // initial layout is done greedily
-        var circles = initialLayout(areas);
-
-        // transform x/y coordinates to a vector to optimize
-        var initial = [], setids = [], setid;
-        for (setid in circles) {
-            if (circles.hasOwnProperty(setid)) {
-                initial.push(circles[setid].x);
-                initial.push(circles[setid].y);
-                setids.push(setid);
-            }
-        }
-
-        // optimize initial layout from our loss function
-        var totalFunctionCalls = 0;
-        var solution = fmin(
-            function(values) {
-                totalFunctionCalls += 1;
-                var current = {};
-                for (var i = 0; i < setids.length; ++i) {
-                    var setid = setids[i];
-                    current[setid] = {x: values[2 * i],
-                                      y: values[2 * i + 1],
-                                      radius : circles[setid].radius,
-                                     // size : circles[setid].size
-                                     };
-                }
-                return lossFunction(current, areas);
-            },
-            initial,
-            parameters);
-
-        // transform solution vector back to x/y points
-        var positions = solution.solution;
-        for (var i = 0; i < setids.length; ++i) {
-            setid = setids[i];
-            circles[setid].x = positions[2 * i];
-            circles[setid].y = positions[2 * i + 1];
-        }
-
-        return circles;
-    }
-
-    var SMALL$1 = 1e-10;
-
-    /** Returns the distance necessary for two circles of radius r1 + r2 to
-    have the overlap area 'overlap' */
-    function distanceFromIntersectArea(r1, r2, overlap) {
-        // handle complete overlapped circles
-        if (Math.min(r1, r2) * Math.min(r1,r2) * Math.PI <= overlap + SMALL$1) {
-            return Math.abs(r1 - r2);
-        }
-
-        return bisect(function(distance) {
-            return circleOverlap(r1, r2, distance) - overlap;
-        }, 0, r1 + r2);
-    }
-
-    /** Missing pair-wise intersection area data can cause problems:
-     treating as an unknown means that sets will be laid out overlapping,
-     which isn't what people expect. To reflect that we want disjoint sets
-     here, set the overlap to 0 for all missing pairwise set intersections */
-    function addMissingAreas(areas) {
-        areas = areas.slice();
-
-        // two circle intersections that aren't defined
-        var ids = [], pairs = {}, i, j, a, b;
-        for (i = 0; i < areas.length; ++i) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                ids.push(area.sets[0]);
-            } else if (area.sets.length == 2) {
-                a = area.sets[0];
-                b = area.sets[1];
-                pairs[[a, b]] = true;
-                pairs[[b, a]] = true;
-            }
-        }
-        ids.sort(function(a, b) { return a > b; });
-
-        for (i = 0; i < ids.length; ++i) {
-            a = ids[i];
-            for (j = i + 1; j < ids.length; ++j) {
-                b = ids[j];
-                if (!([a, b] in pairs)) {
-                    areas.push({'sets': [a, b],
-                                'size': 0});
-                }
-            }
-        }
-        return areas;
-    }
-
-    /// Returns two matrices, one of the euclidean distances between the sets
-    /// and the other indicating if there are subset or disjoint set relationships
-    function getDistanceMatrices(areas, sets, setids) {
-        // initialize an empty distance matrix between all the points
-        var distances = zerosM(sets.length, sets.length),
-            constraints = zerosM(sets.length, sets.length);
-
-        // compute required distances between all the sets such that
-        // the areas match
-        areas.filter(function(x) { return x.sets.length == 2; })
-            .map(function(current) {
-            var left = setids[current.sets[0]],
-                right = setids[current.sets[1]],
-                r1 = Math.sqrt(sets[left].size / Math.PI),
-                r2 = Math.sqrt(sets[right].size / Math.PI),
-                distance = distanceFromIntersectArea(r1, r2, current.size);
-
-            distances[left][right] = distances[right][left] = distance;
-
-            // also update constraints to indicate if its a subset or disjoint
-            // relationship
-            var c = 0;
-            if (current.size + 1e-10 >= Math.min(sets[left].size,
-                                                 sets[right].size)) {
-                c = 1;
-            } else if (current.size <= 1e-10) {
-                c = -1;
-            }
-            constraints[left][right] = constraints[right][left] = c;
-        });
-
-        return {distances: distances, constraints: constraints};
-    }
-
-    /// computes the gradient and loss simulatenously for our constrained MDS optimizer
-    function constrainedMDSGradient(x, fxprime, distances, constraints) {
-        var loss = 0, i;
-        for (i = 0; i < fxprime.length; ++i) {
-            fxprime[i] = 0;
-        }
-
-        for (i = 0; i < distances.length; ++i) {
-            var xi = x[2 * i], yi = x[2 * i + 1];
-            for (var j = i + 1; j < distances.length; ++j) {
-                var xj = x[2 * j], yj = x[2 * j + 1],
-                    dij = distances[i][j],
-                    constraint = constraints[i][j];
-
-                var squaredDistance = (xj - xi) * (xj - xi) + (yj - yi) * (yj - yi),
-                    distance = Math.sqrt(squaredDistance),
-                    delta = squaredDistance - dij * dij;
-
-                if (((constraint > 0) && (distance <= dij)) ||
-                    ((constraint < 0) && (distance >= dij))) {
-                    continue;
-                }
-
-                loss += 2 * delta * delta;
-
-                fxprime[2*i]     += 4 * delta * (xi - xj);
-                fxprime[2*i + 1] += 4 * delta * (yi - yj);
-
-                fxprime[2*j]     += 4 * delta * (xj - xi);
-                fxprime[2*j + 1] += 4 * delta * (yj - yi);
-            }
-        }
-        return loss;
-    }
-
-    /// takes the best working variant of either constrained MDS or greedy
-    function bestInitialLayout(areas, params) {
-        var initial = greedyLayout(areas, params);
-
-        // greedylayout is sufficient for all 2/3 circle cases. try out
-        // constrained MDS for higher order problems, take its output
-        // if it outperforms. (greedy is aesthetically better on 2/3 circles
-        // since it axis aligns)
-        if (areas.length >= 8) {
-            var constrained  = constrainedMDSLayout(areas, params),
-                constrainedLoss = lossFunction(constrained, areas),
-                greedyLoss = lossFunction(initial, areas);
-
-            if (constrainedLoss + 1e-8 < greedyLoss) {
-                initial = constrained;
-            }
-        }
-        return initial;
-    }
-
-    /// use the constrained MDS variant to generate an initial layout
-    function constrainedMDSLayout(areas, params) {
-        params = params || {};
-        var restarts = params.restarts || 10;
-
-        // bidirectionally map sets to a rowid  (so we can create a matrix)
-        var sets = [], setids = {}, i;
-        for (i = 0; i < areas.length; ++i ) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                setids[area.sets[0]] = sets.length;
-                sets.push(area);
-            }
-        }
-
-        var matrices = getDistanceMatrices(areas, sets, setids),
-            distances = matrices.distances,
-            constraints = matrices.constraints;
-
-        // keep distances bounded, things get messed up otherwise.
-        // TODO: proper preconditioner?
-        var norm = norm2(distances.map(norm2))/(distances.length);
-        distances = distances.map(function (row) {
-            return row.map(function (value) { return value / norm; });});
-
-        var obj = function(x, fxprime) {
-            return constrainedMDSGradient(x, fxprime, distances, constraints);
-        };
-
-        var best, current;
-        for (i = 0; i < restarts; ++i) {
-            var initial = zeros(distances.length*2).map(Math.random);
-
-            current = minimizeConjugateGradient(obj, initial, params);
-            if (!best || (current.fx < best.fx)) {
-                best = current;
-            }
-        }
-        var positions = best.x;
-
-        // translate rows back to (x,y,radius) coordinates
-        var circles = {};
-        for (i = 0; i < sets.length; ++i) {
-            var set = sets[i];
-            circles[set.sets[0]] = {
-                x: positions[2*i] * norm,
-                y: positions[2*i + 1] * norm,
-                radius:  Math.sqrt(set.size / Math.PI)
-            };
-        }
-
-        if (params.history) {
-            for (i = 0; i < params.history.length; ++i) {
-                multiplyBy(params.history[i].x, norm);
-            }
-        }
-        return circles;
-    }
-
-    /** Lays out a Venn diagram greedily, going from most overlapped sets to
-    least overlapped, attempting to position each new set such that the
-    overlapping areas to already positioned sets are basically right */
-    function greedyLayout(areas) {
-        // define a circle for each set
-        var circles = {}, setOverlaps = {}, set;
-        for (var i = 0; i < areas.length; ++i) {
-            var area = areas[i];
-            if (area.sets.length == 1) {
-                set = area.sets[0];
-                circles[set] = {x: 1e10, y: 1e10,
-                                rowid: circles.length,
-                                size: area.size,
-                                radius: Math.sqrt(area.size / Math.PI)};
-                setOverlaps[set] = [];
-            }
-        }
-        areas = areas.filter(function(a) { return a.sets.length == 2; });
-
-        // map each set to a list of all the other sets that overlap it
-        for (i = 0; i < areas.length; ++i) {
-            var current = areas[i];
-            var weight = current.hasOwnProperty('weight') ? current.weight : 1.0;
-            var left = current.sets[0], right = current.sets[1];
-
-            // completely overlapped circles shouldn't be positioned early here
-            if (current.size + SMALL$1 >= Math.min(circles[left].size,
-                                                 circles[right].size)) {
-                weight = 0;
-            }
-
-            setOverlaps[left].push ({set:right, size:current.size, weight:weight});
-            setOverlaps[right].push({set:left,  size:current.size, weight:weight});
-        }
-
-        // get list of most overlapped sets
-        var mostOverlapped = [];
-        for (set in setOverlaps) {
-            if (setOverlaps.hasOwnProperty(set)) {
-                var size = 0;
-                for (i = 0; i < setOverlaps[set].length; ++i) {
-                    size += setOverlaps[set][i].size * setOverlaps[set][i].weight;
-                }
-
-                mostOverlapped.push({set: set, size:size});
-            }
-        }
-
-        // sort by size desc
-        function sortOrder(a,b) {
-            return b.size - a.size;
-        }
-        mostOverlapped.sort(sortOrder);
-
-        // keep track of what sets have been laid out
-        var positioned = {};
-        function isPositioned(element) {
-            return element.set in positioned;
-        }
-
-        // adds a point to the output
-        function positionSet(point, index) {
-            circles[index].x = point.x;
-            circles[index].y = point.y;
-            positioned[index] = true;
-        }
-
-        // add most overlapped set at (0,0)
-        positionSet({x: 0, y: 0}, mostOverlapped[0].set);
-
-        // get distances between all points. TODO, necessary?
-        // answer: probably not
-        // var distances = venn.getDistanceMatrices(circles, areas).distances;
-        for (i = 1; i < mostOverlapped.length; ++i) {
-            var setIndex = mostOverlapped[i].set,
-                overlap = setOverlaps[setIndex].filter(isPositioned);
-            set = circles[setIndex];
-            overlap.sort(sortOrder);
-
-            if (overlap.length === 0) {
-                // this shouldn't happen anymore with addMissingAreas
-                throw "ERROR: missing pairwise overlap information";
-            }
-
-            var points = [];
-            for (var j = 0; j < overlap.length; ++j) {
-                // get appropriate distance from most overlapped already added set
-                var p1 = circles[overlap[j].set],
-                    d1 = distanceFromIntersectArea(set.radius, p1.radius,
-                                                   overlap[j].size);
-
-                // sample positions at 90 degrees for maximum aesthetics
-                points.push({x : p1.x + d1, y : p1.y});
-                points.push({x : p1.x - d1, y : p1.y});
-                points.push({y : p1.y + d1, x : p1.x});
-                points.push({y : p1.y - d1, x : p1.x});
-
-                // if we have at least 2 overlaps, then figure out where the
-                // set should be positioned analytically and try those too
-                for (var k = j + 1; k < overlap.length; ++k) {
-                    var p2 = circles[overlap[k].set],
-                        d2 = distanceFromIntersectArea(set.radius, p2.radius,
-                                                       overlap[k].size);
-
-                    var extraPoints = circleCircleIntersection(
-                        { x: p1.x, y: p1.y, radius: d1},
-                        { x: p2.x, y: p2.y, radius: d2});
-
-                    for (var l = 0; l < extraPoints.length; ++l) {
-                        points.push(extraPoints[l]);
-                    }
-                }
-            }
-
-            // we have some candidate positions for the set, examine loss
-            // at each position to figure out where to put it at
-            var bestLoss = 1e50, bestPoint = points[0];
-            for (j = 0; j < points.length; ++j) {
-                circles[setIndex].x = points[j].x;
-                circles[setIndex].y = points[j].y;
-                var loss = lossFunction(circles, areas);
-                if (loss < bestLoss) {
-                    bestLoss = loss;
-                    bestPoint = points[j];
-                }
-            }
-
-            positionSet(bestPoint, setIndex);
-        }
-
-        return circles;
-    }
-
-    /** Given a bunch of sets, and the desired overlaps between these sets - computes
-    the distance from the actual overlaps to the desired overlaps. Note that
-    this method ignores overlaps of more than 2 circles */
-    function lossFunction(sets, overlaps) {
-        var output = 0;
-
-        function getCircles(indices) {
-            return indices.map(function(i) { return sets[i]; });
-        }
-
-        for (var i = 0; i < overlaps.length; ++i) {
-            var area = overlaps[i], overlap;
-            if (area.sets.length == 1) {
-                continue;
-            } else if (area.sets.length == 2) {
-                var left = sets[area.sets[0]],
-                    right = sets[area.sets[1]];
-                overlap = circleOverlap(left.radius, right.radius,
-                                        distance(left, right));
-            } else {
-                overlap = intersectionArea(getCircles(area.sets));
-            }
-
-            var weight = area.hasOwnProperty('weight') ? area.weight : 1.0;
-            output += weight * (overlap - area.size) * (overlap - area.size);
-        }
-
-        return output;
-    }
-
-    // orientates a bunch of circles to point in orientation
-    function orientateCircles(circles, orientation, orientationOrder) {
-        if (orientationOrder === null) {
-            circles.sort(function (a, b) { return b.radius - a.radius; });
-        } else {
-            circles.sort(orientationOrder);
-        }
-
-        var i;
-        // shift circles so largest circle is at (0, 0)
-        if (circles.length > 0) {
-            var largestX = circles[0].x,
-                largestY = circles[0].y;
-
-            for (i = 0; i < circles.length; ++i) {
-                circles[i].x -= largestX;
-                circles[i].y -= largestY;
-            }
-        }
-
-        // rotate circles so that second largest is at an angle of 'orientation'
-        // from largest
-        if (circles.length > 1) {
-            var rotation = Math.atan2(circles[1].x, circles[1].y) - orientation,
-                c = Math.cos(rotation),
-                s = Math.sin(rotation), x, y;
-
-            for (i = 0; i < circles.length; ++i) {
-                x = circles[i].x;
-                y = circles[i].y;
-                circles[i].x = c * x - s * y;
-                circles[i].y = s * x + c * y;
-            }
-        }
-
-        // mirror solution if third solution is above plane specified by
-        // first two circles
-        if (circles.length > 2) {
-            var angle = Math.atan2(circles[2].x, circles[2].y) - orientation;
-            while (angle < 0) { angle += 2* Math.PI; }
-            while (angle > 2*Math.PI) { angle -= 2* Math.PI; }
-            if (angle > Math.PI) {
-                var slope = circles[1].y / (1e-10 + circles[1].x);
-                for (i = 0; i < circles.length; ++i) {
-                    var d = (circles[i].x + slope * circles[i].y) / (1 + slope*slope);
-                    circles[i].x = 2 * d - circles[i].x;
-                    circles[i].y = 2 * d * slope - circles[i].y;
-                }
-            }
-        }
-    }
-
-    function disjointCluster(circles) {
-        // union-find clustering to get disjoint sets
-        circles.map(function(circle) { circle.parent = circle; });
-
-        // path compression step in union find
-        function find(circle) {
-            if (circle.parent !== circle) {
-                circle.parent = find(circle.parent);
-            }
-            return circle.parent;
-        }
-
-        function union(x, y) {
-            var xRoot = find(x), yRoot = find(y);
-            xRoot.parent = yRoot;
-        }
-
-        // get the union of all overlapping sets
-        for (var i = 0; i < circles.length; ++i) {
-            for (var j = i + 1; j < circles.length; ++j) {
-                var maxDistance = circles[i].radius + circles[j].radius;
-                if (distance(circles[i], circles[j]) + 1e-10 < maxDistance) {
-                    union(circles[j], circles[i]);
-                }
-            }
-        }
-
-        // find all the disjoint clusters and group them together
-        var disjointClusters = {}, setid;
-        for (i = 0; i < circles.length; ++i) {
-            setid = find(circles[i]).parent.setid;
-            if (!(setid in disjointClusters)) {
-                disjointClusters[setid] = [];
-            }
-            disjointClusters[setid].push(circles[i]);
-        }
-
-        // cleanup bookkeeping
-        circles.map(function(circle) { delete circle.parent; });
-
-        // return in more usable form
-        var ret = [];
-        for (setid in disjointClusters) {
-            if (disjointClusters.hasOwnProperty(setid)) {
-                ret.push(disjointClusters[setid]);
-            }
-        }
-        return ret;
-    }
-
-    function getBoundingBox(circles) {
-        var minMax = function(d) {
-            var hi = Math.max.apply(null, circles.map(
-                                    function(c) { return c[d] + c.radius; } )),
-                lo = Math.min.apply(null, circles.map(
-                                    function(c) { return c[d] - c.radius;} ));
-            return {max:hi, min:lo};
-        };
-
-        return {xRange: minMax('x'), yRange: minMax('y')};
-    }
-
-    function normalizeSolution(solution, orientation, orientationOrder) {
-        if (orientation === null){
-            orientation = Math.PI/2;
-        }
-
-        // work with a list instead of a dictionary, and take a copy so we
-        // don't mutate input
-        var circles = [], i, setid;
-        for (setid in solution) {
-            if (solution.hasOwnProperty(setid)) {
-                var previous = solution[setid];
-                circles.push({x: previous.x,
-                              y: previous.y,
-                              radius: previous.radius,
-                              setid: setid});
-            }
-        }
-
-        // get all the disjoint clusters
-        var clusters = disjointCluster(circles);
-
-        // orientate all disjoint sets, get sizes
-        for (i = 0; i < clusters.length; ++i) {
-            orientateCircles(clusters[i], orientation, orientationOrder);
-            var bounds = getBoundingBox(clusters[i]);
-            clusters[i].size = (bounds.xRange.max - bounds.xRange.min) * (bounds.yRange.max - bounds.yRange.min);
-            clusters[i].bounds = bounds;
-        }
-        clusters.sort(function(a, b) { return b.size - a.size; });
-
-        // orientate the largest at 0,0, and get the bounds
-        circles = clusters[0];
-        var returnBounds = circles.bounds;
-
-        var spacing = (returnBounds.xRange.max - returnBounds.xRange.min)/50;
-
-        function addCluster(cluster, right, bottom) {
-            if (!cluster) return;
-
-            var bounds = cluster.bounds, xOffset, yOffset, centreing;
-
-            if (right) {
-                xOffset = returnBounds.xRange.max  - bounds.xRange.min + spacing;
-            } else {
-                xOffset = returnBounds.xRange.max  - bounds.xRange.max;
-                centreing = (bounds.xRange.max - bounds.xRange.min) / 2 -
-                            (returnBounds.xRange.max - returnBounds.xRange.min) / 2;
-                if (centreing < 0) xOffset += centreing;
-            }
-
-            if (bottom) {
-                yOffset = returnBounds.yRange.max  - bounds.yRange.min + spacing;
-            } else {
-                yOffset = returnBounds.yRange.max  - bounds.yRange.max;
-                centreing = (bounds.yRange.max - bounds.yRange.min) / 2 -
-                            (returnBounds.yRange.max - returnBounds.yRange.min) / 2;
-                if (centreing < 0) yOffset += centreing;
-            }
-
-            for (var j = 0; j < cluster.length; ++j) {
-                cluster[j].x += xOffset;
-                cluster[j].y += yOffset;
-                circles.push(cluster[j]);
-            }
-        }
-
-        var index = 1;
-        while (index < clusters.length) {
-            addCluster(clusters[index], true, false);
-            addCluster(clusters[index+1], false, true);
-            addCluster(clusters[index+2], true, true);
-            index += 3;
-
-            // have one cluster (in top left). lay out next three relative
-            // to it in a grid
-            returnBounds = getBoundingBox(circles);
-        }
-
-        // convert back to solution form
-        var ret = {};
-        for (i = 0; i < circles.length; ++i) {
-            ret[circles[i].setid] = circles[i];
-        }
-        return ret;
-    }
-
-    /** Scales a solution from venn.venn or venn.greedyLayout such that it fits in
-    a rectangle of width/height - with padding around the borders. also
-    centers the diagram in the available space at the same time */
-    function scaleSolution(solution, width, height, padding) {
-        var circles = [], setids = [];
-        for (var setid in solution) {
-            if (solution.hasOwnProperty(setid)) {
-                setids.push(setid);
-                circles.push(solution[setid]);
-            }
-        }
-
-        width -= 2*padding;
-        height -= 2*padding;
-
-        var bounds = getBoundingBox(circles),
-            xRange = bounds.xRange,
-            yRange = bounds.yRange,
-            xScaling = width  / (xRange.max - xRange.min),
-            yScaling = height / (yRange.max - yRange.min),
-            scaling = Math.min(yScaling, xScaling),
-
-            // while we're at it, center the diagram too
-            xOffset = (width -  (xRange.max - xRange.min) * scaling) / 2,
-            yOffset = (height - (yRange.max - yRange.min) * scaling) / 2;
-
-        var scaled = {};
-        for (var i = 0; i < circles.length; ++i) {
-            var circle = circles[i];
-            scaled[setids[i]] = {
-                radius: scaling * circle.radius,
-                x: padding + xOffset + (circle.x - xRange.min) * scaling,
-                y: padding + yOffset + (circle.y - yRange.min) * scaling,
-            };
-        }
-
-        return scaled;
-    }
-
-    /*global console:true*/
-
-    function VennDiagram() {
-        var width = 600,
-            height = 350,
-            padding = 15,
-            duration = 1000,
-            orientation = Math.PI / 2,
-            normalize = true,
-            wrap = true,
-            styled = true,
-            fontSize = null,
-            orientationOrder = null,
-
-            // mimic the behaviour of d3.scale.category10 from the previous
-            // version of d3
-            colourMap = {},
-
-            // so this is the same as d3.schemeCategory10, which is only defined in d3 4.0
-            // since we can support older versions of d3 as long as we don't force this,
-            // I'm hackily redefining below. TODO: remove this and change to d3.schemeCategory10
-            colourScheme = ["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"],
-            colourIndex = 0,
-            colours = function(key) {
-                if (key in colourMap) {
-                    return colourMap[key];
-                }
-                var ret = colourMap[key] = colourScheme[colourIndex];
-                colourIndex += 1;
-                if (colourIndex >= colourScheme.length) {
-                    colourIndex = 0;
-                }
-                return ret;
-            },
-            layoutFunction = venn;
-
-        function chart(selection) {
-            var data = selection.datum();
-            var solution = layoutFunction(data);
-            if (normalize) {
-                solution = normalizeSolution(solution,
-                                             orientation,
-                                             orientationOrder);
-            }
-            var circles = scaleSolution(solution, width, height, padding);
-            var textCentres = computeTextCentres(circles, data);
-
-            // create svg if not already existing
-            selection.selectAll("svg").data([circles]).enter().append("svg");
-
-            var svg = selection.select("svg")
-                .attr("width", width)
-                .attr("height", height);
-
-            // to properly transition intersection areas, we need the
-            // previous circles locations. load from elements
-            var previous = {}, hasPrevious = false;
-            svg.selectAll("g path").each(function (d) {
-                var path = d3.select(this).attr("d");
-                if ((d.sets.length == 1) && path) {
-                    hasPrevious = true;
-                    previous[d.sets[0]] = circleFromPath(path);
-                }
-            });
-
-            // interpolate intersection area paths between previous and
-            // current paths
-            var pathTween = function(d) {
-                return function(t) {
-                    var c = d.sets.map(function(set) {
-                        var start = previous[set], end = circles[set];
-                        if (!start) {
-                            start = {x : width/2, y : height/2, radius : 1};
-                        }
-                        if (!end) {
-                            end = {x : width/2, y : height/2, radius : 1};
-                        }
-                        return {'x' : start.x * (1 - t) + end.x * t,
-                                'y' : start.y * (1 - t) + end.y * t,
-                                'radius' : start.radius * (1 - t) + end.radius * t};
-                    });
-                    return intersectionAreaPath(c);
-                };
-            };
-
-            // update data, joining on the set ids
-            var nodes = svg.selectAll("g")
-                .data(data, function(d) { return d.sets; });
-
-            // create new nodes
-            var enter = nodes.enter()
-                .append('g')
-                .attr("class", function(d) {
-                    return "venn-area venn-" +
-                        (d.sets.length == 1 ? "circle" : "intersection");
-                })
-                .attr("data-venn-sets", function(d) {
-                    return d.sets.join("_");
-                });
-
-            var enterPath = enter.append("path"),
-                enterText = enter.append("text")
-                .attr("class", "label")
-                .text(function (d) { return label(d); } )
-                .attr("text-anchor", "middle")
-                .attr("dy", ".35em")
-                .attr("x", width/2)
-                .attr("y", height/2);
-
-
-            // apply minimal style if wanted
-            if (styled) {
-                enterPath.style("fill-opacity", "0")
-                    .filter(function (d) { return d.sets.length == 1; } )
-                    .style("fill", function(d) { return colours(label(d)); })
-                    .style("fill-opacity", ".25");
-
-                enterText
-                    .style("fill", function(d) { return d.sets.length == 1 ? colours(label(d)) : "#444"; });
-            }
-
-            // update existing, using pathTween if necessary
-            var update = selection;
-            if (hasPrevious) {
-                update = selection.transition("venn").duration(duration);
-                update.selectAll("path")
-                    .attrTween("d", pathTween);
-            } else {
-                update.selectAll("path")
-                    .attr("d", function(d) {
-                        return intersectionAreaPath(d.sets.map(function (set) { return circles[set]; }));
-                    });
-            }
-
-            var updateText = update.selectAll("text")
-                .filter(function (d) { return d.sets in textCentres; })
-                .text(function (d) { return label(d); } )
-                .attr("x", function(d) { return Math.floor(textCentres[d.sets].x);})
-                .attr("y", function(d) { return Math.floor(textCentres[d.sets].y);});
-
-            if (wrap) {
-                if (hasPrevious) {
-                    // d3 4.0 uses 'on' for events on transitions,
-                    // but d3 3.0 used 'each' instead. switch appropiately
-                    if ('on' in updateText) {
-                        updateText.on("end", wrapText(circles, label));
-                    } else {
-                        updateText.each("end", wrapText(circles, label));
-                    }
-                } else {
-                    updateText.each(wrapText(circles, label));
-                }
-            }
-
-            // remove old
-            var exit = nodes.exit().transition('venn').duration(duration).remove();
-            exit.selectAll("path")
-                .attrTween("d", pathTween);
-
-            var exitText = exit.selectAll("text")
-                .attr("x", width/2)
-                .attr("y", height/2);
-
-            // if we've been passed a fontSize explicitly, use it to
-            // transition
-            if (fontSize !== null) {
-                enterText.style("font-size", "0px");
-                updateText.style("font-size", fontSize);
-                exitText.style("font-size", "0px");
-            }
-
-
-            return {'circles': circles,
-                    'textCentres': textCentres,
-                    'nodes': nodes,
-                    'enter': enter,
-                    'update': update,
-                    'exit': exit};
-        }
-
-        function label(d) {
-            if (d.label) {
-                return d.label;
-            }
-            if (d.sets.length == 1) {
-                return '' + d.sets[0];
-            }
-        }
-
-        chart.wrap = function(_) {
-            if (!arguments.length) return wrap;
-            wrap = _;
-            return chart;
-        };
-
-        chart.width = function(_) {
-            if (!arguments.length) return width;
-            width = _;
-            return chart;
-        };
-
-        chart.height = function(_) {
-            if (!arguments.length) return height;
-            height = _;
-            return chart;
-        };
-
-        chart.padding = function(_) {
-            if (!arguments.length) return padding;
-            padding = _;
-            return chart;
-        };
-
-        chart.colours = function(_) {
-            if (!arguments.length) return colours;
-            colours = _;
-            return chart;
-        };
-
-        chart.fontSize = function(_) {
-            if (!arguments.length) return fontSize;
-            fontSize = _;
-            return chart;
-        };
-
-        chart.duration = function(_) {
-            if (!arguments.length) return duration;
-            duration = _;
-            return chart;
-        };
-
-        chart.layoutFunction = function(_) {
-            if (!arguments.length) return layoutFunction;
-            layoutFunction = _;
-            return chart;
-        };
-
-        chart.normalize = function(_) {
-            if (!arguments.length) return normalize;
-            normalize = _;
-            return chart;
-        };
-
-        chart.styled = function(_) {
-            if (!arguments.length) return styled;
-            styled = _;
-            return chart;
-        };
-
-        chart.orientation = function(_) {
-            if (!arguments.length) return orientation;
-            orientation = _;
-            return chart;
-        };
-
-        chart.orientationOrder = function(_) {
-            if (!arguments.length) return orientationOrder;
-            orientationOrder = _;
-            return chart;
-        };
-
-        return chart;
-    }
-    // sometimes text doesn't fit inside the circle, if thats the case lets wrap
-    // the text here such that it fits
-    // todo: looks like this might be merged into d3 (
-    // https://github.com/mbostock/d3/issues/1642),
-    // also worth checking out is
-    // http://engineering.findthebest.com/wrapping-axis-labels-in-d3-js/
-    // this seems to be one of those things that should be easy but isn't
-    function wrapText(circles, labeller) {
-        return function() {
-            var text = d3.select(this),
-                data = text.datum(),
-                width = circles[data.sets[0]].radius || 50,
-                label = labeller(data) || '';
-
-                var words = label.split(/\s+/).reverse(),
-                maxLines = 3,
-                minChars = (label.length + words.length) / maxLines,
-                word = words.pop(),
-                line = [word],
-                joined,
-                lineNumber = 0,
-                lineHeight = 1.1, // ems
-                tspan = text.text(null).append("tspan").text(word);
-
-            while (true) {
-                word = words.pop();
-                if (!word) break;
-                line.push(word);
-                joined = line.join(" ");
-                tspan.text(joined);
-                if (joined.length > minChars && tspan.node().getComputedTextLength() > width) {
-                    line.pop();
-                    tspan.text(line.join(" "));
-                    line = [word];
-                    tspan = text.append("tspan").text(word);
-                    lineNumber++;
-                }
-            }
-
-            var initial = 0.35 - lineNumber * lineHeight / 2,
-                x = text.attr("x"),
-                y = text.attr("y");
-
-            text.selectAll("tspan")
-                .attr("x", x)
-                .attr("y", y)
-                .attr("dy", function(d, i) {
-                     return (initial + i * lineHeight) + "em";
-                });
-        };
-    }
-
-    function circleMargin(current, interior, exterior) {
-        var margin = interior[0].radius - distance(interior[0], current), i, m;
-        for (i = 1; i < interior.length; ++i) {
-            m = interior[i].radius - distance(interior[i], current);
-            if (m <= margin) {
-                margin = m;
-            }
-        }
-
-        for (i = 0; i < exterior.length; ++i) {
-            m = distance(exterior[i], current) - exterior[i].radius;
-            if (m <= margin) {
-                margin = m;
-            }
-        }
-        return margin;
-    }
-
-    // compute the center of some circles by maximizing the margin of
-    // the center point relative to the circles (interior) after subtracting
-    // nearby circles (exterior)
-    function computeTextCentre(interior, exterior) {
-        // get an initial estimate by sampling around the interior circles
-        // and taking the point with the biggest margin
-        var points = [], i;
-        for (i = 0; i < interior.length; ++i) {
-            var c = interior[i];
-            points.push({x: c.x, y: c.y});
-            points.push({x: c.x + c.radius/2, y: c.y});
-            points.push({x: c.x - c.radius/2, y: c.y});
-            points.push({x: c.x, y: c.y + c.radius/2});
-            points.push({x: c.x, y: c.y - c.radius/2});
-        }
-        var initial = points[0], margin = circleMargin(points[0], interior, exterior);
-        for (i = 1; i < points.length; ++i) {
-            var m = circleMargin(points[i], interior, exterior);
-            if (m >= margin) {
-                initial = points[i];
-                margin = m;
-            }
-        }
-
-        // maximize the margin numerically
-        var solution = fmin(
-                    function(p) { return -1 * circleMargin({x: p[0], y: p[1]}, interior, exterior); },
-                    [initial.x, initial.y],
-                    {maxIterations:500, minErrorDelta:1e-10}).solution;
-        var ret = {x: solution[0], y: solution[1]};
-
-        // check solution, fallback as needed (happens if fully overlapped
-        // etc)
-        var valid = true;
-        for (i = 0; i < interior.length; ++i) {
-            if (distance(ret, interior[i]) > interior[i].radius) {
-                valid = false;
-                break;
-            }
-        }
-
-        for (i = 0; i < exterior.length; ++i) {
-            if (distance(ret, exterior[i]) < exterior[i].radius) {
-                valid = false;
-                break;
-            }
-        }
-
-        if (!valid) {
-            if (interior.length == 1) {
-                ret = {x: interior[0].x, y: interior[0].y};
-            } else {
-                var areaStats = {};
-                intersectionArea(interior, areaStats);
-
-                if (areaStats.arcs.length === 0) {
-                    ret = {'x': 0, 'y': -1000, disjoint:true};
-
-                } else if (areaStats.arcs.length == 1) {
-                    ret = {'x': areaStats.arcs[0].circle.x,
-                           'y': areaStats.arcs[0].circle.y};
-
-                } else if (exterior.length) {
-                    // try again without other circles
-                    ret = computeTextCentre(interior, []);
-
-                } else {
-                    // take average of all the points in the intersection
-                    // polygon. this should basically never happen
-                    // and has some issues:
-                    // https://github.com/benfred/venn.js/issues/48#issuecomment-146069777
-                    ret = getCenter(areaStats.arcs.map(function (a) { return a.p1; }));
-                }
-            }
-        }
-
-        return ret;
-    }
-
-    // given a dictionary of {setid : circle}, returns
-    // a dictionary of setid to list of circles that completely overlap it
-    function getOverlappingCircles(circles) {
-        var ret = {}, circleids = [];
-        for (var circleid in circles) {
-            circleids.push(circleid);
-            ret[circleid] = [];
-        }
-        for (var i  = 0; i < circleids.length; i++) {
-            var a = circles[circleids[i]];
-            for (var j = i + 1; j < circleids.length; ++j) {
-                var b = circles[circleids[j]],
-                    d = distance(a, b);
-
-                if (d + b.radius <= a.radius + 1e-10) {
-                    ret[circleids[j]].push(circleids[i]);
-
-                } else if (d + a.radius <= b.radius + 1e-10) {
-                    ret[circleids[i]].push(circleids[j]);
-                }
-            }
-        }
-        return ret;
-    }
-
-    function computeTextCentres(circles, areas) {
-        var ret = {}, overlapped = getOverlappingCircles(circles);
-        for (var i = 0; i < areas.length; ++i) {
-            var area = areas[i].sets, areaids = {}, exclude = {};
-            for (var j = 0; j < area.length; ++j) {
-                areaids[area[j]] = true;
-                var overlaps = overlapped[area[j]];
-                // keep track of any circles that overlap this area,
-                // and don't consider for purposes of computing the text
-                // centre
-                for (var k = 0; k < overlaps.length; ++k) {
-                    exclude[overlaps[k]] = true;
-                }
-            }
-
-            var interior = [], exterior = [];
-            for (var setid in circles) {
-                if (setid in areaids) {
-                    interior.push(circles[setid]);
-                } else if (!(setid in exclude)) {
-                    exterior.push(circles[setid]);
-                }
-            }
-            var centre = computeTextCentre(interior, exterior);
-            ret[area] = centre;
-            if (centre.disjoint && (areas[i].size > 0)) {
-                console.log("WARNING: area " + area + " not represented on screen");
-            }
-        }
-        return  ret;
-    }
-
-    // sorts all areas in the venn diagram, so that
-    // a particular area is on top (relativeTo) - and
-    // all other areas are so that the smallest areas are on top
-    function sortAreas(div, relativeTo) {
-
-        // figure out sets that are completly overlapped by relativeTo
-        var overlaps = getOverlappingCircles(div.selectAll("svg").datum());
-        var exclude = {};
-        for (var i = 0; i < relativeTo.sets.length; ++i) {
-            var check = relativeTo.sets[i];
-            for (var setid in overlaps) {
-                var overlap = overlaps[setid];
-                for (var j = 0; j < overlap.length; ++j) {
-                    if (overlap[j] == check) {
-                        exclude[setid] = true;
-                        break;
-                    }
-                }
-            }
-        }
-
-        // checks that all sets are in exclude;
-        function shouldExclude(sets) {
-            for (var i = 0; i < sets.length; ++i) {
-                if (!(sets[i] in exclude)) {
-                    return false;
-                }
-            }
-            return true;
-        }
-
-        // need to sort div's so that Z order is correct
-        div.selectAll("g").sort(function (a, b) {
-            // highest order set intersections first
-            if (a.sets.length != b.sets.length) {
-                return a.sets.length - b.sets.length;
-            }
-
-            if (a == relativeTo) {
-                return shouldExclude(b.sets) ? -1 : 1;
-            }
-            if (b == relativeTo) {
-                return shouldExclude(a.sets) ? 1 : -1;
-            }
-
-            // finally by size
-            return b.size - a.size;
-        });
-    }
-
-    function circlePath(x, y, r) {
-        var ret = [];
-        ret.push("\nM", x, y);
-        ret.push("\nm", -r, 0);
-        ret.push("\na", r, r, 0, 1, 0, r *2, 0);
-        ret.push("\na", r, r, 0, 1, 0,-r *2, 0);
-        return ret.join(" ");
-    }
-
-    // inverse of the circlePath function, returns a circle object from an svg path
-    function circleFromPath(path) {
-        var tokens = path.split(' ');
-        return {'x' : parseFloat(tokens[1]),
-                'y' : parseFloat(tokens[2]),
-                'radius' : -parseFloat(tokens[4])
-                };
-    }
-
-    /** returns a svg path of the intersection area of a bunch of circles */
-    function intersectionAreaPath(circles) {
-        var stats = {};
-        intersectionArea(circles, stats);
-        var arcs = stats.arcs;
-
-        if (arcs.length === 0) {
-            return "M 0 0";
-
-        } else if (arcs.length == 1) {
-            var circle = arcs[0].circle;
-            return circlePath(circle.x, circle.y, circle.radius);
-
-        } else {
-            // draw path around arcs
-            var ret = ["\nM", arcs[0].p2.x, arcs[0].p2.y];
-            for (var i = 0; i < arcs.length; ++i) {
-                var arc = arcs[i], r = arc.circle.radius, wide = arc.width > r;
-                ret.push("\nA", r, r, 0, wide ? 1 : 0, 1,
-                         arc.p1.x, arc.p1.y);
-            }
-            return ret.join(" ");
-        }
-    }
-
-    exports.fmin = fmin;
-    exports.minimizeConjugateGradient = minimizeConjugateGradient;
-    exports.bisect = bisect;
-    exports.intersectionArea = intersectionArea;
-    exports.circleCircleIntersection = circleCircleIntersection;
-    exports.circleOverlap = circleOverlap;
-    exports.circleArea = circleArea;
-    exports.distance = distance;
-    exports.circleIntegral = circleIntegral;
-    exports.venn = venn;
-    exports.greedyLayout = greedyLayout;
-    exports.scaleSolution = scaleSolution;
-    exports.normalizeSolution = normalizeSolution;
-    exports.bestInitialLayout = bestInitialLayout;
-    exports.lossFunction = lossFunction;
-    exports.disjointCluster = disjointCluster;
-    exports.distanceFromIntersectArea = distanceFromIntersectArea;
-    exports.VennDiagram = VennDiagram;
-    exports.wrapText = wrapText;
-    exports.computeTextCentres = computeTextCentres;
-    exports.computeTextCentre = computeTextCentre;
-    exports.sortAreas = sortAreas;
-    exports.circlePath = circlePath;
-    exports.circleFromPath = circleFromPath;
-    exports.intersectionAreaPath = intersectionAreaPath;
-
-}));
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/static/logo.png b/config/plugins/visualizations/venn/static/logo.png
deleted file mode 100644
index 3d0b70624c8d..000000000000
Binary files a/config/plugins/visualizations/venn/static/logo.png and /dev/null differ
diff --git a/config/plugins/visualizations/venn/static/logo.svg b/config/plugins/visualizations/venn/static/logo.svg
new file mode 100644
index 000000000000..2d851c8a414c
--- /dev/null
+++ b/config/plugins/visualizations/venn/static/logo.svg
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" height="280" width="380" stroke="#FFFFFF" stroke-width="10">
+ <rect x="2.5" y="2.5" width="375" height="275" fill="#E30A17" rx="50" ry="50"/>
+ <circle cx="140" cy="140" r="100" fill="#FFFFFF"/>
+ <circle cx="240" cy="140" r="100" fill="#E30A17"/>
+ <circle cx="140" cy="140" r="100" fill="none"/>
+</svg>
\ No newline at end of file
diff --git a/config/plugins/visualizations/venn/static/script.css b/config/plugins/visualizations/venn/static/script.css
deleted file mode 100644
index 235c2555cee7..000000000000
--- a/config/plugins/visualizations/venn/static/script.css
+++ /dev/null
@@ -1,14 +0,0 @@
-.venntooltip {
-    position: absolute;
-    text-align: center;
-    width: 128px;
-    height: 22px;
-    background: #333;
-    color: #ddd;
-    border: 0px;
-    border-radius: 8px;
-    opacity: 0;
-}
-.venn-area > .label {
-    font-size: 1em;
-}
\ No newline at end of file
diff --git a/config/plugins/visualizations/vizarr/config/vizarr.xml b/config/plugins/visualizations/vizarr/config/vizarr.xml
new file mode 100644
index 000000000000..5b4b20ffe1a2
--- /dev/null
+++ b/config/plugins/visualizations/vizarr/config/vizarr.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Vizarr Viewer">
+    <description>Basic visualization for Zarr-based images like OME-Zarr</description>
+    <requirements>
+        <requirement type="npm" version="0.1.5" package="@galaxyproject/vizarr"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+
+            <test type="isinstance" test_attr="datatype" result_type="datatype" allow_uri_if_protocol="https,http">data.ZarrDirectory</test>
+            <test type="isinstance" test_attr="datatype" result_type="datatype" allow_uri_if_protocol="https,http">images.OMEZarr</test>
+
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+</visualization>
diff --git a/config/plugins/visualizations/vizarr/static/logo.svg b/config/plugins/visualizations/vizarr/static/logo.svg
new file mode 100644
index 000000000000..83a5214086ea
--- /dev/null
+++ b/config/plugins/visualizations/vizarr/static/logo.svg
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 145.65 126.13">
+  <defs>
+    <style>
+      .cls-1 {
+        fill: #ef4136;
+      }
+
+      .cls-1, .cls-2, .cls-3 {
+        mix-blend-mode: multiply;
+        stroke-width: 0px;
+      }
+
+      .cls-2 {
+        fill: #27aae1;
+      }
+
+      .cls-3 {
+        fill: #39b54a;
+      }
+
+      .cls-4 {
+        isolation: isolate;
+      }
+    </style>
+  </defs>
+  <g class="cls-4">
+    <g id="Layer_2" data-name="Layer 2">
+      <g id="Layer_1-2" data-name="Layer 1">
+        <polygon class="cls-2" points="72.82 40.61 49.38 0 7.5 0 72.82 113.14 138.15 0 96.27 0 72.82 40.61"/>
+        <polygon class="cls-1" points="102.06 12.99 72.82 63.62 43.59 12.99 15 12.99 80.32 126.13 145.65 12.99 102.06 12.99"/>
+        <polygon class="cls-3" points="72.82 63.62 43.59 12.99 0 12.99 65.32 126.13 130.65 12.99 102.06 12.99 72.82 63.62"/>
+      </g>
+    </g>
+  </g>
+</svg>
\ No newline at end of file
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index d4b1170673a1..8ccc68ffb631 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -115,6 +115,14 @@
             "level": "INFO",
             "qualname": "watchdog.observers.inotify_buffer",
         },
+        "py.warnings": {
+            "level": "ERROR",
+            "qualname": "py.warnings",
+        },
+        "celery.utils.functional": {
+            "level": "INFO",
+            "qualname": "celery.utils.functional",
+        },
     },
     "filters": {
         "stack": {
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 91a30ffd171d..722715746ea7 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -984,6 +984,7 @@
     <datatype extension="gmsh.msh" type="galaxy.datatypes.constructive_solid_geometry:GmshMsh" display_in_upload="true"/>
     <datatype extension="gmsh.geo" type="galaxy.datatypes.constructive_solid_geometry:GmshGeo" display_in_upload="true"/>
     <datatype extension="zset.geof" type="galaxy.datatypes.constructive_solid_geometry:ZsetGeof" display_in_upload="true"/>
+    <datatype extension="vtkxml" type="galaxy.datatypes.constructive_solid_geometry:VtkXml" display_in_upload="true"/>
     <datatype extension="stl" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" display_in_upload="true" description="STL is a file format native to the stereolithography CAD software created by 3D Systems."/>
     <!-- Povray script -->
     <datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
@@ -1042,6 +1043,7 @@
     <sniffer type="galaxy.datatypes.mothur:Axes"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
+    <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkXml"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
     <sniffer type="galaxy.datatypes.constructive_solid_geometry:NeperTess"/>
diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py
index 73973abb65a5..9ef0e84ae9ea 100644
--- a/lib/galaxy/datatypes/constructive_solid_geometry.py
+++ b/lib/galaxy/datatypes/constructive_solid_geometry.py
@@ -5,6 +5,7 @@
 """
 
 import abc
+import re
 from typing import (
     List,
     Optional,
@@ -29,6 +30,7 @@
     FilePrefix,
 )
 from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.xml import GenericXml
 
 if TYPE_CHECKING:
     from io import TextIOBase
@@ -189,9 +191,6 @@ class Vtk:
 
     Binary data must be placed into the file immediately after the newline
     ('\\n') character from the previous ASCII keyword and parameter sequence.
-
-    TODO: only legacy formats are currently supported and support for XML formats
-    should be added.
     """
 
     subtype = ""
@@ -813,3 +812,59 @@ def get_next_line(fh):
         # Discard the rest of the line
         fh.readline()
     return line.strip()
+
+
+class VtkXml(GenericXml):
+    """Format for defining VTK (XML based) and its sub-datatypes. https://docs.vtk.org/en/latest/design_documents/VTKFileFormats.html"""
+
+    edam_format = "edam:format_2332"
+    file_ext = "vtkxml"
+
+    # The same MetadataElements are also available for legacy VTK datatypes.
+    MetadataElement(name="vtk_version", default=None, desc="Vtk version", readonly=True, optional=True, visible=True)
+    MetadataElement(name="file_format", default=None, desc="File format", readonly=True, optional=True, visible=True)
+    MetadataElement(name="dataset_type", default=None, desc="Dataset type", readonly=True, optional=True, visible=True)
+
+    def extract_version(self, line: str) -> str:
+        match = re.search(r'version="([^"]+)"', line)
+        if match:
+            return match.group(1)
+        return "?"
+
+    def extract_type(self, line: str) -> str:
+        match = re.search(r'type="([^"]+)"', line)
+        if match:
+            return match.group(1)
+        return "?"
+
+    def set_meta(self, dataset: DatasetProtocol, **kwd) -> None:
+        dataset.metadata.file_format = "XML"
+        with open(dataset.get_file_name(), errors="ignore") as file:
+            # first line might be the xml header, so we take two
+            first_line = file.readline()
+            if first_line.startswith("<?xml"):
+                first_line = file.readline()
+            dataset.metadata.vtk_version = self.extract_version(first_line)
+            dataset.metadata.dataset_type = self.extract_type(first_line)
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        """Set the peek and blurb text for VTK dataset files."""
+        if not dataset.dataset.purged:
+            dataset.peek = "VTK Dataset file"
+            dataset.blurb = f"type {dataset.metadata.dataset_type} version {dataset.metadata.vtk_version}"
+        else:
+            dataset.peek = "File does not exist"
+            dataset.blurb = "File purged from disk"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """Check for the key string 'VTKFile' to determine if this is a VTK dataset file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('data.vtu')
+        >>> VtkXml().sniff(fname)
+        True
+        >>> fname = get_test_fname('1.phyloxml')
+        >>> VtkXml().sniff(fname)
+        False
+        """
+        return self._has_root_element_in_prefix(file_prefix, "VTKFile")
diff --git a/lib/galaxy/datatypes/test/data.vtu b/lib/galaxy/datatypes/test/data.vtu
new file mode 100644
index 000000000000..f9483ba6c0f5
--- /dev/null
+++ b/lib/galaxy/datatypes/test/data.vtu
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="21" NumberOfCells="21">
+      <PointData>
+        <DataArray type="Float64" Name="P_BC_FLOW" format="binary" RangeMin="-2" RangeMax="0">
+          AQAAAACAAACoAAAAFgAAAA==eJxjYCAKHCBAE1JPqvno4gwABYYGwQ==
+        </DataArray>
+        <DataArray type="UInt64" Name="bulk_node_ids" format="binary" RangeMin="0" RangeMax="70">
+          AQAAAACAAACoAAAAOwAAAA==eJwtxRECgDAAAMBJkDQomQySBk2SYNKg/v+kQXdyIfySJ2fP3r34cHTx6tObqy/fbn7c/frzAL7YAwQ=
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="42.42640687119285" RangeMax="94.33981132056604">
+          AQAAAACAAAD4AQAAYwAAAA==eJxjYAABOwcw1RAIoeEAXVzlAIo4gx929XBxqHq4fjT1GOLo6j1xqPdEVQ+31wWHe2Di6OajqccQRzffDlU9hjiaerh5Jmjm+KGKY4QDurgnqjiGv9DVu+BQbwcXBwAoLCke
+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              42.426406871
+            </Value>
+            <Value index="1">
+              94.339811321
+            </Value>
+          </InformationKey>
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="20">
+          AQAAAACAAACoAAAAMQAAAA==eJwtxUECQCAAALAQRSLx/7d2sF0Wwm/y7MXRqzcnZ+8+XHy6+vLt5sfdrz8PMMgA0w==
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="1" RangeMax="21">
+          AQAAAACAAACoAAAAMgAAAA==eJwtxbcBgCAAADArFsAC8v+rDiRLxqGbPHvx6uDNuw+fjk7Ovnz78evi6s/NPzgAAOg=
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="1" RangeMax="1">
+          AQAAAACAAAAVAAAACwAAAA==eJxjZMQCAAD8ABY=
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 4d6c7013e924..c782e31842e2 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -1,12 +1,12 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=dev
 aiohappyeyeballs==2.4.3
-aiohttp==3.10.10
+aiohttp==3.10.11
 aiosignal==1.3.1
 alabaster==0.7.13
 anyio==4.5.2
 ase==3.23.0
-async-timeout==4.0.3 ; python_full_version < '3.11'
+async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==24.2.0
 axe-selenium-python==2.1.6
 babel==2.16.0
@@ -33,19 +33,19 @@ darker==2.1.1
 darkgraylib==1.2.1
 decorator==5.1.1 ; python_full_version >= '3.9'
 defusedxml==0.7.1
-deprecated==1.2.14
+deprecated==1.2.15
 docutils==0.20.1
 dogpile-cache==1.3.3 ; python_full_version >= '3.9'
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 filelock==3.16.1
 fluent-logger==0.11.1
-fonttools==4.54.1
+fonttools==4.55.0
 frozenlist==1.5.0
 galaxy-release-util==0.1.11
 graylint==1.1.1
 greenlet==3.1.1
 h11==0.14.0
-httpcore==1.0.6
+httpcore==1.0.7
 httpx==0.27.2
 idna==3.10
 imagesize==1.4.1
@@ -154,7 +154,7 @@ sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
 sphinx==7.1.2
-sphinx-rtd-theme==3.0.1
+sphinx-rtd-theme==3.0.2
 sphinxcontrib-applehelp==1.0.4
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.1
@@ -169,7 +169,7 @@ testfixtures==8.3.0
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
-tomli==2.0.2 ; python_full_version <= '3.11'
+tomli==2.1.0 ; python_full_version <= '3.11'
 trio==0.27.0
 trio-websocket==0.11.1
 tuspy==1.0.3
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index d063a6f43020..f0afdffeb3c3 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==24.10.31
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.7.3
+ruff==0.7.4
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 342ba9da8659..ce35113d8952 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -6,18 +6,18 @@ aiobotocore==2.15.2
 aiodataloader==0.4.0
 aiofiles==24.1.0
 aiohappyeyeballs==2.4.3
-aiohttp==3.10.10
+aiohttp==3.10.11
 aioitertools==0.12.0
 aiosignal==1.3.1
 alembic==1.14.0
-amqp==5.2.0
+amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.5.2
 apispec==6.6.1
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.5.1
-async-timeout==4.0.3 ; python_full_version < '3.11'
+async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
 attrs==24.2.0
 babel==2.16.0
@@ -64,7 +64,7 @@ dparse==0.6.4
 edam-ontology==1.25.2
 email-validator==2.2.0
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
-fastapi-slim==0.115.4
+fastapi-slim==0.115.5
 filelock==3.16.1
 fissix==24.4.24 ; python_full_version >= '3.13'
 frozenlist==1.5.0
@@ -184,7 +184,7 @@ sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.35
 sqlitedict==2.1.0
-sqlparse==0.5.1
+sqlparse==0.5.2
 starlette==0.41.2
 starlette-context==0.3.6
 starlette-graphene3==0.6.0
@@ -194,7 +194,7 @@ tenacity==9.0.0
 text-unidecode==1.3
 tifffile==2023.7.10
 tinydb==4.8.2
-tomli==2.0.2 ; python_full_version < '3.11'
+tomli==2.1.0 ; python_full_version < '3.11'
 tornado==6.4.1
 tqdm==4.67.0
 tuspy==1.0.3
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index eee703c6e98c..ad5c1328d2c8 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,18 +1,18 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.35.57
-botocore-stubs==1.35.57
+boto3-stubs==1.35.63
+botocore-stubs==1.35.63
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==43.0.3
 lxml-stubs==0.5.1
 mypy==1.13.0
-mypy-boto3-s3==1.35.46
+mypy-boto3-s3==1.35.61
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.9.2
 pydantic-core==2.23.4
-tomli==2.0.2 ; python_full_version < '3.11'
+tomli==2.1.0 ; python_full_version < '3.11'
 types-awscrt==0.23.0
 types-bleach==6.1.0.20240331
 types-boto==2.49.18.20241019
@@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20240917
 types-requests==2.31.0.6
 types-s3transfer==0.10.3
-types-setuptools==75.3.0.20241107
+types-setuptools==75.5.0.20241116
 types-six==1.16.21.20241105
 types-urllib3==1.26.25.14
 typing-extensions==4.12.2
diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
index 12078ddbed3d..201f510ee9b6 100755
--- a/lib/galaxy/dependencies/update.sh
+++ b/lib/galaxy/dependencies/update.sh
@@ -38,7 +38,7 @@ uv="${uv_venv}/bin/uv"
 if [ -n "$pkg" ]; then
     ${uv} lock --upgrade-package "$pkg"
 else
-    ${uv} lock
+    ${uv} lock --upgrade
 fi
 
 # Update pinned requirements files.
diff --git a/lib/galaxy/files/sources/__init__.py b/lib/galaxy/files/sources/__init__.py
index 19fcc1b21475..fd1e84670173 100644
--- a/lib/galaxy/files/sources/__init__.py
+++ b/lib/galaxy/files/sources/__init__.py
@@ -277,6 +277,10 @@ def to_dict(self, for_serialization=False, user_context: "OptionalUserContext" =
         context doesn't need to be present after the plugin is re-hydrated.
         """
 
+    @abc.abstractmethod
+    def prefer_links(self) -> bool:
+        """Prefer linking to files."""
+
 
 class SupportsBrowsing(metaclass=abc.ABCMeta):
     """An interface indicating that this filesource is browsable.
@@ -351,6 +355,9 @@ def user_has_access(self, user_context: "OptionalUserContext") -> bool:
             or (self._user_has_required_roles(user_context) and self._user_has_required_groups(user_context))
         )
 
+    def prefer_links(self) -> bool:
+        return False
+
     @property
     def user_context_required(self) -> bool:
         return self.requires_roles is not None or self.requires_groups is not None
diff --git a/lib/galaxy/files/sources/posix.py b/lib/galaxy/files/sources/posix.py
index 8768b5b5ca9c..258d5ef20a69 100644
--- a/lib/galaxy/files/sources/posix.py
+++ b/lib/galaxy/files/sources/posix.py
@@ -26,6 +26,7 @@
 DEFAULT_ENFORCE_SYMLINK_SECURITY = True
 DEFAULT_DELETE_ON_REALIZE = False
 DEFAULT_ALLOW_SUBDIR_CREATION = True
+DEFAULT_PREFER_LINKS = False
 
 
 class PosixFilesSourceProperties(FilesSourceProperties, total=False):
@@ -33,6 +34,7 @@ class PosixFilesSourceProperties(FilesSourceProperties, total=False):
     enforce_symlink_security: bool
     delete_on_realize: bool
     allow_subdir_creation: bool
+    prefer_links: bool
 
 
 class PosixFilesSource(BaseFilesSource):
@@ -53,6 +55,10 @@ def __init__(self, **kwd: Unpack[PosixFilesSourceProperties]):
         self.enforce_symlink_security = props.get("enforce_symlink_security", DEFAULT_ENFORCE_SYMLINK_SECURITY)
         self.delete_on_realize = props.get("delete_on_realize", DEFAULT_DELETE_ON_REALIZE)
         self.allow_subdir_creation = props.get("allow_subdir_creation", DEFAULT_ALLOW_SUBDIR_CREATION)
+        self._prefer_links = props.get("prefer_links", DEFAULT_PREFER_LINKS)
+
+    def prefer_links(self) -> bool:
+        return self._prefer_links
 
     def _list(
         self,
@@ -182,6 +188,7 @@ def _serialization_props(self, user_context: OptionalUserContext = None) -> Posi
             "enforce_symlink_security": self.enforce_symlink_security,
             "delete_on_realize": self.delete_on_realize,
             "allow_subdir_creation": self.allow_subdir_creation,
+            "prefer_links": self._prefer_links,
         }
 
     @property
diff --git a/lib/galaxy/files/uris.py b/lib/galaxy/files/uris.py
index d35e51d696c4..9d48853294d6 100644
--- a/lib/galaxy/files/uris.py
+++ b/lib/galaxy/files/uris.py
@@ -49,8 +49,7 @@ def stream_url_to_file(
     target_path: Optional[str] = None,
     file_source_opts: Optional[FilesSourceOptions] = None,
 ) -> str:
-    if file_sources is None:
-        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    file_sources = ensure_file_sources(file_sources)
     file_source, rel_path = file_sources.get_file_source_path(url)
     if file_source:
         if not target_path:
@@ -62,6 +61,12 @@ def stream_url_to_file(
         raise NoMatchingFileSource(f"Could not find a matching handler for: {url}")
 
 
+def ensure_file_sources(file_sources: Optional["ConfiguredFileSources"]) -> "ConfiguredFileSources":
+    if file_sources is None:
+        file_sources = ConfiguredFileSources.from_dict(None, load_stock_plugins=True)
+    return file_sources
+
+
 def stream_to_file(stream, suffix="", prefix="", dir=None, text=False, **kwd):
     """Writes a stream to a temporary file, returns the temporary file's name"""
     fd, temp_name = tempfile.mkstemp(suffix=suffix, prefix=prefix, dir=dir, text=text)
diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py
index a638202d0ec3..a2bb8ff6c76b 100644
--- a/lib/galaxy/jobs/runners/pulsar.py
+++ b/lib/galaxy/jobs/runners/pulsar.py
@@ -1027,7 +1027,7 @@ class PulsarMQJobRunner(PulsarJobRunner):
 
 
 DEFAULT_PULSAR_CONTAINER = "galaxy/pulsar-pod-staging:0.15.0.2"
-COEXECUTION_DESTENTATION_DEFAULTS = {
+COEXECUTION_DESTINATION_DEFAULTS = {
     "default_file_action": "remote_transfer",
     "rewrite_parameters": "true",
     "jobs_directory": "/pulsar_staging",
@@ -1039,7 +1039,7 @@ class PulsarMQJobRunner(PulsarJobRunner):
 
 
 class PulsarCoexecutionJobRunner(PulsarMQJobRunner):
-    destination_defaults = COEXECUTION_DESTENTATION_DEFAULTS
+    destination_defaults = COEXECUTION_DESTINATION_DEFAULTS
 
     def _populate_parameter_defaults(self, job_destination):
         super()._populate_parameter_defaults(job_destination)
@@ -1053,7 +1053,7 @@ def _populate_parameter_defaults(self, job_destination):
             pulsar_app_config["staging_directory"] = params.get("jobs_directory")
 
 
-KUBERNETES_DESTINATION_DEFAULTS: Dict[str, Any] = {"k8s_enabled": True, **COEXECUTION_DESTENTATION_DEFAULTS}
+KUBERNETES_DESTINATION_DEFAULTS: Dict[str, Any] = {"k8s_enabled": True, **COEXECUTION_DESTINATION_DEFAULTS}
 
 
 class PulsarKubernetesJobRunner(PulsarCoexecutionJobRunner):
@@ -1061,14 +1061,14 @@ class PulsarKubernetesJobRunner(PulsarCoexecutionJobRunner):
     poll = True  # Poll so we can check API for pod IP for ITs.
 
 
-TES_DESTENTATION_DEFAULTS: Dict[str, Any] = {
+TES_DESTINATION_DEFAULTS: Dict[str, Any] = {
     "tes_url": PARAMETER_SPECIFICATION_REQUIRED,
-    **COEXECUTION_DESTENTATION_DEFAULTS,
+    **COEXECUTION_DESTINATION_DEFAULTS,
 }
 
 
 class PulsarTesJobRunner(PulsarCoexecutionJobRunner):
-    destination_defaults = TES_DESTENTATION_DEFAULTS
+    destination_defaults = TES_DESTINATION_DEFAULTS
 
 
 class PulsarRESTJobRunner(PulsarJobRunner):
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 48be30372d67..20354c029198 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -1078,6 +1078,7 @@ def _workflow_to_dict_run(self, trans, stored, workflow, history=None):
             step_models.append(step_model)
         return {
             "id": trans.app.security.encode_id(stored.id),
+            "workflow_id": trans.app.security.encode_id(workflow.id),
             "history_id": trans.app.security.encode_id(history.id) if history else None,
             "name": stored.name,
             "owner": stored.user.username,
diff --git a/lib/galaxy/schema/invocation.py b/lib/galaxy/schema/invocation.py
index 8872889ac078..76d7ca72761f 100644
--- a/lib/galaxy/schema/invocation.py
+++ b/lib/galaxy/schema/invocation.py
@@ -90,6 +90,7 @@ class FailureReason(str, Enum):
     expression_evaluation_failed = "expression_evaluation_failed"
     when_not_boolean = "when_not_boolean"
     unexpected_failure = "unexpected_failure"
+    workflow_parameter_invalid = "workflow_parameter_invalid"
 
 
 # The reasons below are attached to the invocation and user-actionable.
@@ -225,6 +226,14 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     )
 
 
+class GenericInvocationFailureWorkflowParameterInvalid(InvocationFailureMessageBase[DatabaseIdT], Generic[DatabaseIdT]):
+    reason: Literal[FailureReason.workflow_parameter_invalid]
+    workflow_step_id: int = Field(
+        ..., title="Workflow parameter step that failed validation", validation_alias="workflow_step_index"
+    )
+    details: str = Field(..., description="Message raised by validator")
+
+
 InvocationCancellationReviewFailed = GenericInvocationCancellationReviewFailed[int]
 InvocationCancellationHistoryDeleted = GenericInvocationCancellationHistoryDeleted[int]
 InvocationCancellationUserRequest = GenericInvocationCancellationUserRequest[int]
@@ -236,6 +245,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationFailureWhenNotBoolean = GenericInvocationFailureWhenNotBoolean[int]
 InvocationUnexpectedFailure = GenericInvocationUnexpectedFailure[int]
 InvocationWarningWorkflowOutputNotFound = GenericInvocationEvaluationWarningWorkflowOutputNotFound[int]
+InvocationFailureWorkflowParameterInvalid = GenericInvocationFailureWorkflowParameterInvalid[int]
 
 InvocationMessageUnion = Union[
     InvocationCancellationReviewFailed,
@@ -249,6 +259,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
     InvocationFailureWhenNotBoolean,
     InvocationUnexpectedFailure,
     InvocationWarningWorkflowOutputNotFound,
+    InvocationFailureWorkflowParameterInvalid,
 ]
 
 InvocationCancellationReviewFailedResponseModel = GenericInvocationCancellationReviewFailed[EncodedDatabaseIdField]
@@ -266,6 +277,9 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
 InvocationWarningWorkflowOutputNotFoundResponseModel = GenericInvocationEvaluationWarningWorkflowOutputNotFound[
     EncodedDatabaseIdField
 ]
+InvocationFailureWorkflowParameterInvalidResponseModel = GenericInvocationFailureWorkflowParameterInvalid[
+    EncodedDatabaseIdField
+]
 
 _InvocationMessageResponseUnion = Annotated[
     Union[
@@ -280,6 +294,7 @@ class GenericInvocationEvaluationWarningWorkflowOutputNotFound(
         InvocationFailureWhenNotBooleanResponseModel,
         InvocationUnexpectedFailureResponseModel,
         InvocationWarningWorkflowOutputNotFoundResponseModel,
+        InvocationFailureWorkflowParameterInvalidResponseModel,
     ],
     Field(discriminator="reason"),
 ]
diff --git a/lib/galaxy/tool_shed/tools/tool_validator.py b/lib/galaxy/tool_shed/tools/tool_validator.py
index a73af2230c9e..428601c65113 100644
--- a/lib/galaxy/tool_shed/tools/tool_validator.py
+++ b/lib/galaxy/tool_shed/tools/tool_validator.py
@@ -97,7 +97,7 @@ def load_tool_from_config(self, repository_id, full_path):
             tool = None
             valid = False
             error_message = (
-                f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file.  Upload a file '
+                f'This file requires an entry for "{str(e)}" in the tool_data_table_conf.xml file. Upload a file '
             )
             error_message += (
                 "named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct "
diff --git a/lib/galaxy/tool_util/parser/factory.py b/lib/galaxy/tool_util/parser/factory.py
index f36647dfd40d..ce403638f7f0 100644
--- a/lib/galaxy/tool_util/parser/factory.py
+++ b/lib/galaxy/tool_util/parser/factory.py
@@ -119,17 +119,22 @@ def get_tool_source_from_representation(tool_format, tool_representation):
         raise Exception(f"Unknown tool representation format [{tool_format}].")
 
 
-def get_input_source(content):
+def get_input_source(content, trusted: bool = True):
     """Wrap dicts or XML elements as InputSource if needed.
 
     If the supplied content is already an InputSource object,
     it is simply returned. This allow Galaxy to uniformly
     consume using the tool input source interface.
+
+    Setting trusted to false indicates that no dynamic code should be
+    executed - no eval. This should be used for user-defined tools (in
+    the future) and for workflow inputs.
     """
     if not isinstance(content, InputSource):
         if isinstance(content, dict):
-            content = YamlInputSource(content)
+            content = YamlInputSource(content, trusted=trusted)
         else:
+            assert trusted  # trust is not implemented for XML inputs
             content = XmlInputSource(content)
     return content
 
diff --git a/lib/galaxy/tool_util/parser/parameter_validators.py b/lib/galaxy/tool_util/parser/parameter_validators.py
index 6525b7d90fb8..ca539f74ee1d 100644
--- a/lib/galaxy/tool_util/parser/parameter_validators.py
+++ b/lib/galaxy/tool_util/parser/parameter_validators.py
@@ -2,6 +2,7 @@
 from typing import (
     Any,
     cast,
+    Dict,
     List,
     Optional,
     Sequence,
@@ -14,6 +15,7 @@
     Field,
     model_validator,
     PrivateAttr,
+    TypeAdapter,
 )
 from typing_extensions import (
     Annotated,
@@ -96,6 +98,9 @@ class ParameterValidatorModel(StrictModel):
     implicit: bool = False
     _static: bool = PrivateAttr(False)
     _deprecated: bool = PrivateAttr(False)
+    # validators must be explicitly set as 'safe' to operate as user-defined workflow parameters or to be used
+    # within future user-defined tool parameters
+    _safe: bool = PrivateAttr(False)
 
     @model_validator(mode="after")
     def set_default_message(self) -> Self:
@@ -163,6 +168,7 @@ class RegexParameterValidatorModel(StaticValidatorModel):
     type: Literal["regex"] = "regex"
     negate: Negate = NEGATE_DEFAULT
     expression: Annotated[str, ValidationArgument("Regular expression to validate against.", xml_body=True)]
+    _safe: bool = PrivateAttr(True)
 
     @property
     def default_message(self) -> str:
@@ -189,6 +195,7 @@ class InRangeParameterValidatorModel(StaticValidatorModel):
     exclude_min: bool = False
     exclude_max: bool = False
     negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
 
     def statically_validate(self, value: Any):
         if isinstance(value, (int, float)):
@@ -211,7 +218,9 @@ def default_message(self) -> str:
             op1 = "<"
         if self.exclude_max:
             op2 = "<"
-        range_description_str = f"({self.min} {op1} value {op2} {self.max})"
+        min_str = str(self.min) if self.min is not None else "-infinity"
+        max_str = str(self.max) if self.max is not None else "+infinity"
+        range_description_str = f"({min_str} {op1} value {op2} {max_str})"
         return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"
 
 
@@ -220,6 +229,7 @@ class LengthParameterValidatorModel(StaticValidatorModel):
     min: Optional[int] = None
     max: Optional[int] = None
     negate: Negate = NEGATE_DEFAULT
+    _safe: bool = PrivateAttr(True)
 
     def statically_validate(self, value: Any):
         if isinstance(value, str):
@@ -458,6 +468,20 @@ def default_message(self) -> str:
 ]
 
 
+DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
+
+
+def parse_dict_validators(validator_dicts: List[Dict[str, Any]], trusted: bool) -> List[AnyValidatorModel]:
+    validator_models = []
+    for validator_dict in validator_dicts:
+        validator = DiscriminatedAnyValidatorModel.validate_python(validator_dict)
+        if not trusted:
+            # Don't risk instantiating unsafe validators for user-defined code
+            assert validator._safe
+        validator_models.append(validator)
+    return validator_models
+
+
 def parse_xml_validators(input_elem: Element) -> List[AnyValidatorModel]:
     validator_els: List[Element] = input_elem.findall("validator") or []
     models = []
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index c2e6352384c0..88be9c72846a 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -34,6 +34,10 @@
     ToolOutputCollection,
     ToolOutputCollectionStructure,
 )
+from .parameter_validators import (
+    AnyValidatorModel,
+    parse_dict_validators,
+)
 from .stdio import error_on_exit_code
 from .util import is_dict
 
@@ -329,8 +333,9 @@ def parse_input_sources(self):
 
 
 class YamlInputSource(InputSource):
-    def __init__(self, input_dict):
+    def __init__(self, input_dict, trusted: bool = True):
         self.input_dict = input_dict
+        self.trusted = trusted
 
     def get(self, key, default=None):
         return self.input_dict.get(key, default)
@@ -378,6 +383,9 @@ def parse_when_input_sources(self):
             sources.append((value, case_page_source))
         return sources
 
+    def parse_validators(self) -> List[AnyValidatorModel]:
+        return parse_dict_validators(self.input_dict.get("validators", []), trusted=self.trusted)
+
     def parse_static_options(self) -> List[Tuple[str, str, bool]]:
         static_options = []
         input_dict = self.input_dict
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 8975b36408ec..0890052b56a0 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -68,6 +68,10 @@ List of behavior changes associated with profile versions:
 - Do not use Galaxy python environment for `data_source_async` tools.
 - Drop request parameters received by data source tools that are not declared in `<request_param_translation>` section.
 
+### 24.2
+
+- require a valid `data_ref` attribute for `data_column` parameters
+
 ### Examples
 
 A normal tool:
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index af9aed7c604e..2e352e7c0f39 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -135,7 +135,6 @@
     DataCollectionToolParameter,
     DataToolParameter,
     HiddenToolParameter,
-    ImplicitConversionRequired,
     SelectTagParameter,
     SelectToolParameter,
     ToolParameter,
@@ -154,6 +153,7 @@
 )
 from galaxy.tools.parameters.input_translation import ToolInputTranslator
 from galaxy.tools.parameters.meta import expand_meta_parameters
+from galaxy.tools.parameters.populate_model import populate_model
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.tools.parameters.wrapped_json import json_wrap
 from galaxy.util import (
@@ -1665,8 +1665,9 @@ def parse_param_elem(self, input_source: InputSource, enctypes, context) -> Tool
         # form when it changes
         for name in param.get_dependencies():
             # Let it throw exception, but give some hint what the problem might be
-            if name not in context:
-                log.error(f"Tool with id '{self.id}': Could not find dependency '{name}' of parameter '{param.name}'")
+            assert (
+                name in context
+            ), f"Tool with id '{self.id}': Could not find dependency '{name}' of parameter '{param.name}'"
             context[name].refresh_on_change = True
         return param
 
@@ -2690,63 +2691,13 @@ def populate_model(self, request_context, inputs, state_inputs, group_inputs, ot
         """
         Populates the tool model consumed by the client form builder.
         """
-        other_values = ExpressionContext(state_inputs, other_values)
-        for input_index, input in enumerate(inputs.values()):
-            tool_dict = None
-            group_state = state_inputs.get(input.name, {})
-            if input.type == "repeat":
-                tool_dict = input.to_dict(request_context)
-                group_size = len(group_state)
-                tool_dict["cache"] = [None] * group_size
-                group_cache: List[List[str]] = tool_dict["cache"]
-                for i in range(group_size):
-                    group_cache[i] = []
-                    self.populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
-            elif input.type == "conditional":
-                tool_dict = input.to_dict(request_context)
-                if "test_param" in tool_dict:
-                    test_param = tool_dict["test_param"]
-                    test_param["value"] = input.test_param.value_to_basic(
-                        group_state.get(
-                            test_param["name"], input.test_param.get_initial_value(request_context, other_values)
-                        ),
-                        self.app,
-                    )
-                    test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
-                    for i in range(len(tool_dict["cases"])):
-                        current_state = {}
-                        if i == group_state.get("__current_case__"):
-                            current_state = group_state
-                        self.populate_model(
-                            request_context,
-                            input.cases[i].inputs,
-                            current_state,
-                            tool_dict["cases"][i]["inputs"],
-                            other_values,
-                        )
-            elif input.type == "section":
-                tool_dict = input.to_dict(request_context)
-                self.populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
-            else:
-                try:
-                    initial_value = input.get_initial_value(request_context, other_values)
-                    tool_dict = input.to_dict(request_context, other_values=other_values)
-                    tool_dict["value"] = input.value_to_basic(
-                        state_inputs.get(input.name, initial_value), self.app, use_security=True
-                    )
-                    tool_dict["default_value"] = input.value_to_basic(initial_value, self.app, use_security=True)
-                    tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
-                except ImplicitConversionRequired:
-                    tool_dict = input.to_dict(request_context)
-                    # This hack leads client to display a text field
-                    tool_dict["textable"] = True
-                except Exception:
-                    tool_dict = input.to_dict(request_context)
-                    log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
-            if input_index >= len(group_inputs):
-                group_inputs.append(tool_dict)
-            else:
-                group_inputs[input_index] = tool_dict
+        populate_model(
+            request_context=request_context,
+            inputs=inputs,
+            state_inputs=state_inputs,
+            group_inputs=group_inputs,
+            other_values=other_values,
+        )
 
     def _map_source_to_history(self, trans, tool_inputs, params):
         # Need to remap dataset parameters. Job parameters point to original
diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index bd5f1ae0b8e6..bad82540d7fa 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -23,6 +23,7 @@
     UploadProblemException,
 )
 from galaxy.files.uris import (
+    ensure_file_sources,
     stream_to_file,
     stream_url_to_file,
 )
@@ -97,13 +98,13 @@ def expand_elements_from(target_or_item):
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _directory_to_items(decompressed_directory)
             elif elements_from == "bagit":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _bagit_to_items(elements_from_path)
             elif elements_from == "bagit_archive":
                 decompressed_directory = _decompress_target(upload_config, target_or_item)
                 items = _bagit_to_items(decompressed_directory)
             elif elements_from == "directory":
-                _, elements_from_path = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
+                _, elements_from_path, _ = _has_src_to_path(upload_config, target_or_item, is_dataset=False)
                 items = _directory_to_items(elements_from_path)
             else:
                 raise Exception(f"Unknown elements from type encountered [{elements_from}]")
@@ -205,7 +206,7 @@ def _resolve_item(item):
                     pass
                 key = keys[composite_item_idx]
                 writable_file = writable_files[key]
-                _, src_target = _has_src_to_path(upload_config, composite_item)
+                _, src_target, _ = _has_src_to_path(upload_config, composite_item)
                 # do the writing
                 sniff.handle_composite_file(
                     datatype,
@@ -238,10 +239,23 @@ def _resolve_item_with_primary(item):
         converted_path = None
 
         deferred = upload_config.get_option(item, "deferred")
+
+        link_data_only = upload_config.link_data_only
+        link_data_only_explicit = upload_config.link_data_only_explicit
+        if "link_data_only" in item:
+            # Allow overriding this on a per file basis.
+            link_data_only, link_data_only_explicit = _link_data_only(item)
+
         name: str
         path: Optional[str]
+        default_in_place = False
         if not deferred:
-            name, path = _has_src_to_path(upload_config, item, is_dataset=True)
+            name, path, is_link = _has_src_to_path(
+                upload_config, item, is_dataset=True, link_data_only_explicitly_set=link_data_only_explicit
+            )
+            if is_link:
+                link_data_only = True
+                default_in_place = True
         else:
             name, path = _has_src_to_name(item) or "Deferred Dataset", None
         sources = []
@@ -266,10 +280,6 @@ def _resolve_item_with_primary(item):
                     item["error_message"] = error_message
 
         dbkey = item.get("dbkey", "?")
-        link_data_only = upload_config.link_data_only
-        if "link_data_only" in item:
-            # Allow overriding this on a per file basis.
-            link_data_only = _link_data_only(item)
 
         ext = "data"
         staged_extra_files = None
@@ -281,7 +291,7 @@ def _resolve_item_with_primary(item):
 
         effective_state = "ok"
         if not deferred and not error_message:
-            in_place = item.get("in_place", False)
+            in_place = item.get("in_place", default_in_place)
             purge_source = item.get("purge_source", True)
 
             registry = upload_config.registry
@@ -339,7 +349,7 @@ def walk_extra_files(items, prefix=""):
                                 item_prefix = os.path.join(prefix, name)
                             walk_extra_files(item.get("elements"), prefix=item_prefix)
                         else:
-                            src_name, src_path = _has_src_to_path(upload_config, item)
+                            src_name, src_path, _ = _has_src_to_path(upload_config, item)
                             if prefix:
                                 rel_path = os.path.join(prefix, src_name)
                             else:
@@ -425,7 +435,7 @@ def _bagit_to_items(directory):
 
 
 def _decompress_target(upload_config: "UploadConfig", target: Dict[str, Any]):
-    elements_from_name, elements_from_path = _has_src_to_path(upload_config, target, is_dataset=False)
+    elements_from_name, elements_from_path, _ = _has_src_to_path(upload_config, target, is_dataset=False)
     # by default Galaxy will check for a directory with a single file and interpret that
     # as the new root for expansion, this is a good user experience for uploading single
     # files in a archive but not great from an API perspective. Allow disabling by setting
@@ -483,13 +493,33 @@ def _has_src_to_name(item) -> Optional[str]:
     return name
 
 
-def _has_src_to_path(upload_config: "UploadConfig", item: Dict[str, Any], is_dataset: bool = False) -> Tuple[str, str]:
+def _has_src_to_path(
+    upload_config: "UploadConfig",
+    item: Dict[str, Any],
+    is_dataset: bool = False,
+    link_data_only: bool = False,
+    link_data_only_explicitly_set: bool = False,
+) -> Tuple[str, str, bool]:
     assert "src" in item, item
     src = item.get("src")
     name = item.get("name")
+    is_link = False
     if src == "url":
         url = item.get("url")
+        file_sources = ensure_file_sources(upload_config.file_sources)
         assert url, "url cannot be empty"
+        if not link_data_only_explicitly_set:
+            file_source, rel_path = file_sources.get_file_source_path(url)
+            prefer_links = file_source.prefer_links()
+            if prefer_links:
+                if rel_path.startswith("/"):
+                    rel_path = rel_path[1:]
+                path = os.path.abspath(os.path.join(file_source.root, rel_path))
+                if name is None:
+                    name = url.split("/")[-1]
+                is_link = True
+                return name, path, is_link
+
         try:
             path = stream_url_to_file(url, file_sources=upload_config.file_sources, dir=upload_config.working_directory)
         except Exception as e:
@@ -513,7 +543,7 @@ def _has_src_to_path(upload_config: "UploadConfig", item: Dict[str, Any], is_dat
         path = item["path"]
         if name is None:
             name = os.path.basename(path)
-    return name, path
+    return name, path, is_link
 
 
 def _handle_hash_validation(hash_function: HashFunctionNameEnum, hash_value: str, path: str):
@@ -564,7 +594,7 @@ def __init__(
         self.space_to_tab = request.get("space_to_tab", False)
         self.auto_decompress = request.get("auto_decompress", False)
         self.deferred = request.get("deferred", False)
-        self.link_data_only = _link_data_only(request)
+        self.link_data_only, self.link_data_only_explicit = _link_data_only(request)
         self.file_sources_dict = file_sources_dict
         self._file_sources = None
 
@@ -616,12 +646,19 @@ def ensure_in_working_directory(self, path, purge_source, in_place):
         return new_path
 
 
-def _link_data_only(has_config_dict):
-    link_data_only = has_config_dict.get("link_data_only", False)
-    if not isinstance(link_data_only, bool):
-        # Allow the older string values of 'copy_files' and 'link_to_files'
-        link_data_only = link_data_only == "copy_files"
-    return link_data_only
+def _link_data_only(has_config_dict) -> Tuple[bool, bool]:
+    if "link_data_only" in has_config_dict:
+        link_data_only_raw = has_config_dict["link_data_only"]
+        if not isinstance(link_data_only_raw, bool):
+            # Allow the older string values of 'copy_files' and 'link_to_files'
+            link_data_only = link_data_only_raw == "copy_files"
+        else:
+            link_data_only = link_data_only_raw
+        link_data_only_explicit = True
+    else:
+        link_data_only = False
+        link_data_only_explicit = False
+    return link_data_only, link_data_only_explicit
 
 
 def _for_each_src(f, obj):
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d3bb7f119c58..6b35473959e4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -146,7 +146,7 @@ def assert_throws_param_value_error(message):
 
 class ParameterValueError(ValueError):
     def __init__(self, message_suffix, parameter_name, parameter_value=NO_PARAMETER_VALUE, is_dynamic=None):
-        message = f"parameter '{parameter_name}': {message_suffix}"
+        message = f"Parameter '{parameter_name}': {message_suffix}"
         super().__init__(message)
         self.message_suffix = message_suffix
         self.parameter_name = parameter_name
@@ -175,11 +175,11 @@ class ToolParameter(UsesDictVisibleKeys):
     >>> trans = Bunch(app=None)
     >>> p = ToolParameter(None, XML('<param argument="--parameter-name" type="text" value="default" />'))
     >>> assert p.name == 'parameter_name'
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
     """
 
     name: str
-    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "refresh_on_change"]
+    dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "help_format", "refresh_on_change"]
 
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
@@ -193,6 +193,7 @@ def __init__(self, tool, input_source, context=None):
         self.is_dynamic = False
         self.label = input_source.parse_label()
         self.help = input_source.parse_help()
+        self.help_format = input_source.get("help_format") or "html"
         if (sanitizer_elem := input_source.parse_sanitizer_elem()) is not None:
             self.sanitizer = ToolParameterSanitizer.from_element(sanitizer_elem)
         else:
@@ -316,7 +317,7 @@ def validate(self, value, trans=None) -> None:
             try:
                 validator.validate(value, trans)
             except ValueError as e:
-                raise ValueError(f"Parameter {self.name}: {e}") from None
+                raise ParameterValueError(str(e), self.name, value) from None
 
     def to_dict(self, trans, other_values=None):
         """to_dict tool parameter. This can be overridden by subclasses."""
@@ -388,7 +389,7 @@ class TextToolParameter(SimpleTextToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
+    [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
     """
 
     def __init__(self, tool, input_source):
@@ -445,9 +446,9 @@ class IntegerToolParameter(TextToolParameter):
     >>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
     >>> assert type(p.from_json("10", trans)) == int
-    >>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
+    >>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
     ...     p.from_json("_string", trans)
     """
 
@@ -518,9 +519,9 @@ class FloatToolParameter(TextToolParameter):
     >>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
     >>> assert type(p.from_json("36.1", trans)) == float
-    >>> with assert_throws_param_value_error("parameter '_name': an integer or workflow parameter is required"):
+    >>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
     ...     p.from_json("_string", trans)
     """
 
@@ -593,7 +594,7 @@ class BooleanToolParameter(ToolParameter):
     >>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
     >>> print(p.from_json('true', trans))
     True
     >>> print(p.to_param_dict_string(True))
@@ -667,7 +668,7 @@ class FileToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
+    [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
     """
 
     def __init__(self, tool, input_source):
@@ -741,7 +742,7 @@ class FTPFileToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
+    [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
     """
 
     def __init__(self, tool, input_source):
@@ -814,7 +815,7 @@ class HiddenToolParameter(ToolParameter):
     >>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
     """
 
     def __init__(self, tool, input_source):
@@ -841,14 +842,14 @@ class ColorToolParameter(ToolParameter):
     _name
     >>> print(p.to_param_dict_string("#ffffff"))
     #ffffff
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
     >>> p = ColorToolParameter(None, XML('<param name="_name" type="color"/>'))
     >>> print(p.get_initial_value(trans, {}))
     #000000
     >>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
     >>> print(p.to_param_dict_string("#ffffff"))
     (255, 255, 255)
-    >>> with assert_throws_param_value_error("parameter '_name': Failed to convert 'None' to RGB."):
+    >>> with assert_throws_param_value_error("Parameter '_name': Failed to convert 'None' to RGB."):
     ...      p.to_param_dict_string(None)
     """
 
@@ -882,7 +883,7 @@ class BaseURLToolParameter(HiddenToolParameter):
     >>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
     >>> print(p.name)
     _name
-    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
+    >>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
     """
 
     def __init__(self, tool, input_source):
@@ -932,7 +933,7 @@ class SelectToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
+    [('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
     >>> p = SelectToolParameter(None, XML(
     ... '''
     ... <param name="_name" type="select" multiple="true">
@@ -944,7 +945,7 @@ class SelectToolParameter(ToolParameter):
     >>> print(p.name)
     _name
     >>> sorted(p.to_dict(trans).items())
-    [('argument', None), ('display', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
+    [('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
     >>> print(p.to_param_dict_string(["y", "z"]))
     y,z
     """
@@ -1403,6 +1404,10 @@ def __init__(self, tool, input_source):
         if self.accept_default:
             self.optional = True
         self.data_ref = input_source.get("data_ref", None)
+        profile = tool.profile if tool else None
+        assert (
+            profile is None or Version(str(profile)) < Version("24.2") or self.data_ref is not None
+        ), f"data_column parameter {self.name} requires a valid data_ref attribute"
         self.ref_input = None
         # Legacy style default value specification...
         self.default_value = input_source.get("default_value", None)
@@ -1970,7 +1975,7 @@ def do_validate(v):
                     try:
                         validator.validate(v, trans)
                     except ValueError as e:
-                        raise ValueError(f"Parameter {self.name}: {e}") from None
+                        raise ParameterValueError(str(e), self.name, v) from None
 
         dataset_count = 0
         if value:
diff --git a/lib/galaxy/tools/parameters/populate_model.py b/lib/galaxy/tools/parameters/populate_model.py
new file mode 100644
index 000000000000..41950bc3a03f
--- /dev/null
+++ b/lib/galaxy/tools/parameters/populate_model.py
@@ -0,0 +1,74 @@
+import logging
+from typing import (
+    Any,
+    Dict,
+    List,
+)
+
+from galaxy.util.expressions import ExpressionContext
+from .basic import ImplicitConversionRequired
+
+log = logging.getLogger(__name__)
+
+
+def populate_model(request_context, inputs, state_inputs, group_inputs: List[Dict[str, Any]], other_values=None):
+    """
+    Populates the tool model consumed by the client form builder.
+    """
+    other_values = ExpressionContext(state_inputs, other_values)
+    for input_index, input in enumerate(inputs.values()):
+        tool_dict = None
+        group_state = state_inputs.get(input.name, {})
+        if input.type == "repeat":
+            tool_dict = input.to_dict(request_context)
+            group_size = len(group_state)
+            tool_dict["cache"] = [None] * group_size
+            group_cache: List[List[Dict[str, Any]]] = tool_dict["cache"]
+            for i in range(group_size):
+                group_cache[i] = []
+                populate_model(request_context, input.inputs, group_state[i], group_cache[i], other_values)
+        elif input.type == "conditional":
+            tool_dict = input.to_dict(request_context)
+            if "test_param" in tool_dict:
+                test_param = tool_dict["test_param"]
+                test_param["value"] = input.test_param.value_to_basic(
+                    group_state.get(
+                        test_param["name"], input.test_param.get_initial_value(request_context, other_values)
+                    ),
+                    request_context.app,
+                )
+                test_param["text_value"] = input.test_param.value_to_display_text(test_param["value"])
+                for i in range(len(tool_dict["cases"])):
+                    current_state = {}
+                    if i == group_state.get("__current_case__"):
+                        current_state = group_state
+                    populate_model(
+                        request_context,
+                        input.cases[i].inputs,
+                        current_state,
+                        tool_dict["cases"][i]["inputs"],
+                        other_values,
+                    )
+        elif input.type == "section":
+            tool_dict = input.to_dict(request_context)
+            populate_model(request_context, input.inputs, group_state, tool_dict["inputs"], other_values)
+        else:
+            try:
+                initial_value = input.get_initial_value(request_context, other_values)
+                tool_dict = input.to_dict(request_context, other_values=other_values)
+                tool_dict["value"] = input.value_to_basic(
+                    state_inputs.get(input.name, initial_value), request_context.app, use_security=True
+                )
+                tool_dict["default_value"] = input.value_to_basic(initial_value, request_context.app, use_security=True)
+                tool_dict["text_value"] = input.value_to_display_text(tool_dict["value"])
+            except ImplicitConversionRequired:
+                tool_dict = input.to_dict(request_context)
+                # This hack leads client to display a text field
+                tool_dict["textable"] = True
+            except Exception:
+                tool_dict = input.to_dict(request_context)
+                log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
+        if input_index >= len(group_inputs):
+            group_inputs.append(tool_dict)
+        else:
+            group_inputs[input_index] = tool_dict
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 895cd1dfadef..57e0a6c45f10 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -233,7 +233,7 @@ class MetadataEqualValidator(Validator):
 
     requires_dataset_metadata = True
 
-    def __init__(self, metadata_name=None, value=None, message=None, negate="false"):
+    def __init__(self, metadata_name=None, value=None, message=None, negate: bool = False):
         super().__init__(message, negate)
         self.metadata_name = metadata_name
         self.value = value
@@ -381,7 +381,7 @@ class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
     """
 
     def __init__(
-        self, tool_data_table, metadata_column: Union[str, int], message="Value already present.", negate="false"
+        self, tool_data_table, metadata_column: Union[str, int], message="Value already present.", negate: bool = False
     ):
         super().__init__(tool_data_table, metadata_column, message, negate)
 
diff --git a/lib/galaxy/visualization/plugins/plugin.py b/lib/galaxy/visualization/plugins/plugin.py
index e3bdf0e03d3c..bcd8c57098c7 100644
--- a/lib/galaxy/visualization/plugins/plugin.py
+++ b/lib/galaxy/visualization/plugins/plugin.py
@@ -80,12 +80,11 @@ def __init__(self, app, path, name, config, context=None, **kwargs):
         base_url = context.get("base_url", "")
         self.base_url = "/".join((base_url, self.name)) if base_url else self.name
         self.static_path = self._get_static_path(self.path)
-        if self.static_path and os.path.exists(os.path.join(self.static_path, "logo.png")):
-            self.config["logo"] = f"{self.static_path}/logo.png"
         template_cache_dir = context.get("template_cache_dir", None)
         additional_template_paths = context.get("additional_template_paths", [])
         self._set_up_template_plugin(template_cache_dir, additional_template_paths=additional_template_paths)
         self.resource_parser = resource_parser.ResourceParser(app)
+        self._set_logo()
 
     def render(self, trans=None, embedded=None, **kwargs):
         """
@@ -232,6 +231,15 @@ def _parse_embedded(self, embedded):
         # as is for now
         return embedded
 
+    def _set_logo(self):
+        if self.static_path:
+            supported_formats = ["png", "svg"]
+            for file_format in supported_formats:
+                logo_path = os.path.join(self.static_path, f"logo.{file_format}")
+                if os.path.isfile(logo_path):
+                    self.config["logo"] = logo_path
+                    return
+
 
 class ScriptVisualizationPlugin(VisualizationPlugin):
     """
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index a530b7769978..f39167a84253 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -41,6 +41,16 @@ class VisualizationController(
     def __init__(self, app: StructuredApp):
         super().__init__(app)
 
+    def get_visualization(self, trans, visualization_id, check_ownership=True, check_accessible=False):
+        """
+        Get a Visualization from the database by id, verifying ownership.
+        """
+        visualization = trans.sa_session.get(model.Visualization, trans.security.decode_id(visualization_id))
+        if not visualization:
+            raise MessageException("Visualization not found")
+        else:
+            return self.security_check(trans, visualization, check_ownership, check_accessible)
+
     #
     # -- Functions for operating on visualizations. --
     #
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index f210755d0482..22d469fd8c80 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -4,15 +4,19 @@
 
 import json
 import logging
+import math
 import re
 from collections import defaultdict
 from typing import (
     Any,
     cast,
     Dict,
+    get_args,
     Iterable,
     List,
+    Literal,
     Optional,
+    Tuple,
     Type,
     TYPE_CHECKING,
     Union,
@@ -47,8 +51,10 @@
     InvocationFailureExpressionEvaluationFailed,
     InvocationFailureOutputNotFound,
     InvocationFailureWhenNotBoolean,
+    InvocationFailureWorkflowParameterInvalid,
 )
 from galaxy.tool_util.cwl.util import set_basename_and_derived_properties
+from galaxy.tool_util.parser import get_input_source
 from galaxy.tool_util.parser.output_objects import ToolExpressionOutput
 from galaxy.tools import (
     DatabaseOperationTool,
@@ -70,7 +76,6 @@
 from galaxy.tools.parameters.basic import (
     BaseDataToolParameter,
     BooleanToolParameter,
-    ColorToolParameter,
     DataCollectionToolParameter,
     DataToolParameter,
     FloatToolParameter,
@@ -84,8 +89,10 @@
 from galaxy.tools.parameters.grouping import (
     Conditional,
     ConditionalWhen,
+    Repeat,
 )
 from galaxy.tools.parameters.history_query import HistoryQuery
+from galaxy.tools.parameters.populate_model import populate_model
 from galaxy.tools.parameters.workflow_utils import (
     ConnectedValue,
     is_runtime_value,
@@ -102,6 +109,7 @@
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import fill_template
 from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
+from galaxy.workflow.workflow_parameter_input_definitions import get_default_parameter
 
 if TYPE_CHECKING:
     from galaxy.schema.invocation import InvocationMessageUnion
@@ -117,6 +125,9 @@
 # ones.
 RUNTIME_POST_JOB_ACTIONS_KEY = "__POST_JOB_ACTIONS__"
 
+INPUT_PARAMETER_TYPES = Literal["text", "integer", "float", "boolean", "color"]
+POSSIBLE_PARAMETER_TYPES: Tuple[INPUT_PARAMETER_TYPES] = get_args(INPUT_PARAMETER_TYPES)
+
 
 class NoReplacement:
     def __str__(self):
@@ -910,7 +921,7 @@ def to_dict(self, *args, **kwds):
         return as_dict
 
 
-def optional_param(optional):
+def optional_param(optional=None):
     bool_source = dict(name="optional", label="Optional", type="boolean", checked=optional)
     optional_value = BooleanToolParameter(None, bool_source)
     return optional_value
@@ -1179,7 +1190,7 @@ def _parse_state_into_dict(self):
 
 
 class InputParameterModule(WorkflowModule):
-    POSSIBLE_PARAMETER_TYPES = ["text", "integer", "float", "boolean", "color"]
+    POSSIBLE_PARAMETER_TYPES = POSSIBLE_PARAMETER_TYPES
     type = "parameter_input"
     name = "Input parameter"
     default_parameter_type = "text"
@@ -1192,7 +1203,6 @@ class InputParameterModule(WorkflowModule):
     def get_inputs(self):
         parameter_def = self._parse_state_into_dict()
         parameter_type = parameter_def["parameter_type"]
-        optional = parameter_def["optional"]
         select_source = dict(name="parameter_type", label="Parameter type", type="select", value=parameter_type)
         select_source["options"] = [
             {"value": "text", "label": "Text"},
@@ -1214,54 +1224,10 @@ def get_inputs(self):
         parameter_type_cond.test_param = input_parameter_type
         cases = []
 
-        for param_type in ["text", "integer", "float", "boolean", "color"]:
-            default_source: Dict[str, Union[int, float, bool, str]] = dict(
-                name="default", label="Default Value", type=param_type
-            )
-            if param_type == "text":
-                if parameter_type == "text":
-                    text_default = parameter_def.get("default") or ""
-                else:
-                    text_default = ""
-                default_source["value"] = text_default
-                input_default_value: Union[
-                    TextToolParameter,
-                    IntegerToolParameter,
-                    FloatToolParameter,
-                    BooleanToolParameter,
-                    ColorToolParameter,
-                ] = TextToolParameter(None, default_source)
-            elif param_type == "integer":
-                if parameter_type == "integer":
-                    integer_default = parameter_def.get("default") or 0
-                else:
-                    integer_default = 0
-                default_source["value"] = integer_default
-                input_default_value = IntegerToolParameter(None, default_source)
-            elif param_type == "float":
-                if parameter_type == "float":
-                    float_default = parameter_def.get("default") or 0.0
-                else:
-                    float_default = 0.0
-                default_source["value"] = float_default
-                input_default_value = FloatToolParameter(None, default_source)
-            elif param_type == "boolean":
-                if parameter_type == "boolean":
-                    boolean_default = parameter_def.get("default") or False
-                else:
-                    boolean_default = False
-                default_source["value"] = boolean_default
-                default_source["checked"] = boolean_default
-                input_default_value = BooleanToolParameter(None, default_source)
-            elif param_type == "color":
-                if parameter_type == "color":
-                    color_default = parameter_def.get("default") or "#000000"
-                else:
-                    color_default = "#000000"
-                default_source["value"] = color_default
-                input_default_value = ColorToolParameter(None, default_source)
+        for param_type in POSSIBLE_PARAMETER_TYPES:
+            default_parameter = get_default_parameter(param_type)
 
-            optional_value = optional_param(optional)
+            optional_value = optional_param()
             optional_cond = Conditional("optional")
             optional_cond.test_param = optional_value
 
@@ -1270,9 +1236,10 @@ def get_inputs(self):
             when_this_type.inputs = {}
             when_this_type.inputs["optional"] = optional_cond
 
-            specify_default_checked = "default" in parameter_def
             specify_default_source = dict(
-                name="specify_default", label="Specify a default value", type="boolean", checked=specify_default_checked
+                name="specify_default",
+                label="Specify a default value",
+                type="boolean",
             )
             specify_default = BooleanToolParameter(None, specify_default_source)
             specify_default_cond = Conditional("specify_default")
@@ -1281,7 +1248,7 @@ def get_inputs(self):
             when_specify_default_true = ConditionalWhen()
             when_specify_default_true.value = "true"
             when_specify_default_true.inputs = {}
-            when_specify_default_true.inputs["default"] = input_default_value
+            when_specify_default_true.inputs["default"] = default_parameter
 
             when_specify_default_false = ConditionalWhen()
             when_specify_default_false.value = "false"
@@ -1309,43 +1276,62 @@ def get_inputs(self):
                     label="Allow multiple selection",
                     help="Only applies when connected to multi-select parameter(s)",
                     type="boolean",
-                    checked=parameter_def.get("multiple", False),
                 )
+
                 specify_multiple = BooleanToolParameter(None, specify_multiple_source)
+
+                add_validators_repeat = Repeat("validators")
+                add_validators_repeat.title = "Add validator to restrict valid input"
+                add_validators_repeat.min = 0
+                add_validators_repeat.max = math.inf
+                add_validators_repeat.inputs = {
+                    "regex_match": TextToolParameter(
+                        None,
+                        {
+                            "optional": False,
+                            "name": "regex_match",
+                            "label": "Specify regular expression",
+                            "help": "Provided [regular expression](gxhelp://programming.python.reg.ex) must match input value for input to be valid",
+                            "help_format": "markdown",
+                        },
+                    ),
+                    "regex_doc": TextToolParameter(
+                        None,
+                        {
+                            "optional": False,
+                            "name": "regex_doc",
+                            "label": "Specify a message",
+                            "help": "This message will be shown if the regular does not match the input",
+                        },
+                    ),
+                }
+
                 # Insert multiple option as first option, which is determined by dictionary insert order
-                when_this_type.inputs = {"multiple": specify_multiple, **when_this_type.inputs}
+                when_this_type.inputs = {
+                    "multiple": specify_multiple,
+                    "validators": add_validators_repeat,
+                    **when_this_type.inputs,
+                }
 
                 restrict_how_source: Dict[str, Union[str, List[Dict[str, Union[str, bool]]]]] = dict(
                     name="how", label="Restrict Text Values?", type="select"
                 )
-                if parameter_def.get("restrictions") is not None:
-                    restrict_how_value = "staticRestrictions"
-                elif parameter_def.get("restrictOnConnections") is True:
-                    restrict_how_value = "onConnections"
-                elif parameter_def.get("suggestions") is not None:
-                    restrict_how_value = "staticSuggestions"
-                else:
-                    restrict_how_value = "none"
                 restrict_how_source["options"] = [
                     {
                         "value": "none",
                         "label": "Do not specify restrictions (default).",
-                        "selected": restrict_how_value == "none",
                     },
                     {
                         "value": "onConnections",
                         "label": "Attempt restriction based on connections.",
-                        "selected": restrict_how_value == "onConnections",
                     },
                     {
                         "value": "staticRestrictions",
                         "label": "Provide list of all possible values.",
-                        "selected": restrict_how_value == "staticRestrictions",
                     },
                     {
                         "value": "staticSuggestions",
                         "label": "Provide list of suggested values.",
-                        "selected": restrict_how_value == "staticSuggestions",
                     },
                 ]
                 restrictions_cond = Conditional("restrictions")
@@ -1403,11 +1389,56 @@ def get_inputs(self):
                 restrictions_cond.cases = restrictions_cond_cases
                 when_this_type.inputs["restrictions"] = restrictions_cond
 
+            if param_type == "integer":
+                when_this_type.inputs["min"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = IntegerToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+            if param_type == "float":
+                when_this_type.inputs["min"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "min",
+                        "optional": True,
+                        "value": parameter_def.get("min", ""),
+                        "label": "Set a minimum value for this input",
+                    },
+                )
+                when_this_type.inputs["max"] = FloatToolParameter(
+                    None,
+                    {
+                        "name": "max",
+                        "optional": True,
+                        "value": parameter_def.get("max", ""),
+                        "label": "Set a maximum value for this input",
+                    },
+                )
+
             cases.append(when_this_type)
 
         parameter_type_cond.cases = cases
         return {"parameter_definition": parameter_type_cond}
 
+    def get_config_form(self, step=None):
+        """Serializes input parameters of a module into input dictionaries."""
+        group_inputs: List[Dict[str, Any]] = []
+        populate_model(self.trans, self.get_inputs(), self.state.inputs, group_inputs)
+        return {"title": self.name, "inputs": group_inputs}
+
     def restrict_options(self, step, connections: Iterable[WorkflowStepConnection], default_value):
         try:
             static_options = []
@@ -1511,6 +1542,9 @@ def _parameter_def_list_to_options(parameter_value):
             parameter_kwds["options"] = _parameter_def_list_to_options(restriction_values)
             restricted_inputs = True
 
+        if parameter_def.get("validators"):
+            parameter_kwds["validators"] = parameter_def["validators"]
+
         client_parameter_type = parameter_type
         if restricted_inputs:
             client_parameter_type = "select"
@@ -1529,9 +1563,10 @@ def _parameter_def_list_to_options(parameter_value):
             suggestion_values = parameter_def.get("suggestions")
             parameter_kwds["options"] = _parameter_def_list_to_options(suggestion_values)
 
-        input_source = dict(
+        input_source_dict = dict(
             name="input", label=self.label, type=client_parameter_type, optional=optional, **parameter_kwds
         )
+        input_source = get_input_source(input_source_dict, trusted=False)
         input = parameter_class(None, input_source)
         return dict(input=input)
 
@@ -1560,7 +1595,10 @@ def execute(
         self, trans, progress: "WorkflowProgress", invocation_step, use_cached_job: bool = False
     ) -> Optional[bool]:
         step = invocation_step.workflow_step
-        input_value = step.state.inputs["input"]
+        if step.id in progress.inputs_by_step_id:
+            input_value = progress.inputs_by_step_id[step.id]
+        else:
+            input_value = step.state.inputs["input"]
         if input_value is None:
             default_value = step.get_input_default_value(NO_REPLACEMENT)
             # TODO: look at parameter type and infer if value should be a dictionary
@@ -1569,6 +1607,16 @@ def execute(
             if not isinstance(default_value, dict):
                 default_value = {"value": default_value}
             input_value = default_value.get("value", NO_REPLACEMENT)
+        input_param = self.get_runtime_inputs(self)["input"]
+        # TODO: raise DelayedWorkflowEvaluation if replacement not ready ? Need test
+        try:
+            input_param.validate(input_value)
+        except ValueError as e:
+            raise FailWorkflowEvaluation(
+                why=InvocationFailureWorkflowParameterInvalid(
+                    reason=FailureReason.workflow_parameter_invalid, workflow_step_id=step.id, details=str(e)
+                )
+            )
         step_outputs = dict(output=input_value)
         progress.set_outputs_for_input(invocation_step, step_outputs)
         return None
@@ -1581,6 +1629,7 @@ def step_state_to_tool_state(self, state):
             default_value = state["default"]
             state["optional"] = True
         multiple = state.get("multiple")
+        source_validators = state.get("validators")
         restrictions = state.get("restrictions")
         restrictOnConnections = state.get("restrictOnConnections")
         suggestions = state.get("suggestions")
@@ -1600,6 +1649,23 @@ def step_state_to_tool_state(self, state):
         }
         if multiple is not None:
             state["parameter_definition"]["multiple"] = multiple
+        if source_validators is not None:
+            form_validators = []
+            # the form definition can change from Galaxy to Galaxy fairly freely, but the source validators are persisted
+            # and need to be consistent - here we convert the persisted/YAML tool definition version to the "tool form" version.
+            for source_validator in source_validators:
+                source_type = source_validator["type"]
+                if source_type == "regex":
+                    form_validators.append(
+                        {
+                            "regex_doc": source_validator.get("message"),
+                            "regex_match": source_validator.get("expression"),
+                        }
+                    )
+                elif source_type == "in_range":
+                    state["parameter_definition"]["min"] = source_validator.get("min")
+                    state["parameter_definition"]["max"] = source_validator.get("max")
+            state["parameter_definition"]["validators"] = form_validators
         state["parameter_definition"]["restrictions"] = {}
         state["parameter_definition"]["restrictions"]["how"] = restrictions_how
 
@@ -1643,6 +1709,32 @@ def _parse_state_into_dict(self):
                 optional = False
             if "multiple" in parameters_def:
                 rval["multiple"] = parameters_def["multiple"]
+            source_validators = []
+            if "min" in parameters_def or "max" in parameters_def:
+                min = parameters_def.get("min")
+                max = parameters_def.get("max")
+                source_validators.append(
+                    {
+                        "min": min,
+                        "max": max,
+                        "negate": False,
+                        "type": "in_range",
+                    }
+                )
+
+            if "validators" in parameters_def:
+                form_validators = parameters_def["validators"]
+                # convert the current tool form structure to the persisted YAML-definition style
+                for form_validator in form_validators:
+                    source_validators.append(
+                        {
+                            "message": form_validator["regex_doc"],
+                            "expression": form_validator["regex_match"],
+                            "negate": False,
+                            "type": "regex",
+                        }
+                    )
+            rval["validators"] = source_validators
             restrictions_cond_values = parameters_def.get("restrictions")
             if restrictions_cond_values:
 
diff --git a/lib/galaxy/workflow/run_request.py b/lib/galaxy/workflow/run_request.py
index b8f6b753a924..a6ca78e3d28c 100644
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -28,7 +28,9 @@
     transaction,
 )
 from galaxy.tool_util.parameters import DataRequestUri
+from galaxy.tools.parameters.basic import ParameterValueError
 from galaxy.tools.parameters.meta import expand_workflow_inputs
+from galaxy.workflow.modules import WorkflowModuleInjector
 from galaxy.workflow.resources import get_resource_mapper_function
 
 if TYPE_CHECKING:
@@ -368,11 +370,20 @@ def build_workflow_run_configs(
 
         steps_by_id = workflow.steps_by_id
         # Set workflow inputs.
+        module_injector = WorkflowModuleInjector(trans, False)
         for key, input_dict in normalized_inputs.items():
             if input_dict is None:
                 continue
             step = steps_by_id[key]
             if step.type == "parameter_input":
+                module_injector.inject(step)
+                input_param = step.module.get_runtime_inputs(step.module)["input"]
+                try:
+                    input_param.validate(input_dict)
+                except ParameterValueError as e:
+                    raise exceptions.RequestParameterInvalidException(
+                        f"{step.label or step.order_index + 1}: {e.message_suffix}"
+                    )
                 continue
             if "src" not in input_dict:
                 raise exceptions.RequestParameterInvalidException(
diff --git a/lib/galaxy/workflow/workflow_parameter_input_definitions.py b/lib/galaxy/workflow/workflow_parameter_input_definitions.py
new file mode 100644
index 000000000000..2b31e793e40e
--- /dev/null
+++ b/lib/galaxy/workflow/workflow_parameter_input_definitions.py
@@ -0,0 +1,48 @@
+from typing import (
+    Dict,
+    Literal,
+    Union,
+)
+
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    ColorToolParameter,
+    FloatToolParameter,
+    IntegerToolParameter,
+    TextToolParameter,
+)
+
+param_types = Literal["text", "integer", "float", "color", "boolean"]
+default_source_type = Dict[str, Union[int, float, bool, str]]
+tool_param_type = Union[
+    TextToolParameter,
+    IntegerToolParameter,
+    FloatToolParameter,
+    BooleanToolParameter,
+    ColorToolParameter,
+]
+
+
+def get_default_parameter(param_type: param_types) -> tool_param_type:
+    """
+    param_type is the type of parameter we want to build up, stored_parameter_type is the parameter_type
+    as stored in the tool state
+    """
+    default_source: default_source_type = dict(name="default", label="Default Value", type=param_type, optional=False)
+    if param_type == "text":
+        input_default_value: Union[
+            TextToolParameter,
+            IntegerToolParameter,
+            FloatToolParameter,
+            BooleanToolParameter,
+            ColorToolParameter,
+        ] = TextToolParameter(None, default_source)
+    elif param_type == "integer":
+        input_default_value = IntegerToolParameter(None, default_source)
+    elif param_type == "float":
+        input_default_value = FloatToolParameter(None, default_source)
+    elif param_type == "boolean":
+        input_default_value = BooleanToolParameter(None, default_source)
+    elif param_type == "color":
+        input_default_value = ColorToolParameter(None, default_source)
+    return input_default_value
diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py
index c904e808f70f..9c16fc18eb72 100644
--- a/lib/galaxy_test/api/test_jobs.py
+++ b/lib/galaxy_test/api/test_jobs.py
@@ -634,7 +634,7 @@ def test_submission_on_collection_with_deleted_element(self, history_id):
         assert response.status_code == 400
         assert (
             response.json()["err_msg"]
-            == "parameter 'collection': the previously selected dataset collection has elements that are deleted."
+            == "Parameter 'collection': the previously selected dataset collection has elements that are deleted."
         )
 
     @pytest.mark.require_new_history
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 6be4ea256490..41d982d246c9 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -934,7 +934,7 @@ def test_data_column_defaults(self):
             with self.dataset_populator.test_history(require_new=False) as history_id:
                 response = self._run("gx_data_column_multiple", history_id, inputs, assert_ok=False).json()
                 assert "err_msg" in response, str(response)
-                assert "parameter 'parameter': an invalid option" in response["err_msg"]
+                assert "Parameter 'parameter': an invalid option" in response["err_msg"]
 
             with self.dataset_populator.test_history(require_new=True) as history_id:
                 response = self._run("gx_data_column_optional", history_id, inputs, assert_ok=True)
@@ -2217,7 +2217,7 @@ def test_implicit_conversion_and_reduce_invalid_param(self):
                 self._run_implicit_collection_and_reduce(history_id=history_id, param="X")
         details = self.dataset_populator.get_history_dataset_details(history_id=history_id, hid=3, assert_ok=False)
         assert details["state"] == "error"
-        assert "parameter 'col': an invalid option" in details["misc_info"]
+        assert "Parameter 'col': an invalid option" in details["misc_info"]
 
     def _run_implicit_collection_and_reduce(self, history_id, param):
         fasta_path = self.test_data_resolver.get_filename("1.fasta")
diff --git a/lib/galaxy_test/driver/integration_setup.py b/lib/galaxy_test/driver/integration_setup.py
index b63b567247ea..30194e63c830 100644
--- a/lib/galaxy_test/driver/integration_setup.py
+++ b/lib/galaxy_test/driver/integration_setup.py
@@ -15,7 +15,9 @@
 REQUIRED_GROUP_EXPRESSION = f"{GROUP_A} or '{GROUP_B}'"
 
 
-def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include_test_data_dir: bool) -> str:
+def get_posix_file_source_config(
+    root_dir: str, roles: str, groups: str, include_test_data_dir: bool, prefer_links: bool = False
+) -> str:
     rval = f"""
 - type: posix
   id: posix_test
@@ -26,6 +28,17 @@ def get_posix_file_source_config(root_dir: str, roles: str, groups: str, include
   requires_roles: {roles}
   requires_groups: {groups}
 """
+    if prefer_links:
+        rval += f"""
+- type: posix
+  id: linking_source
+  label: Posix
+  doc: Files from local path to links
+  root: {root_dir}
+  writable: true
+  prefer_links: true
+"""
+
     if include_test_data_dir:
         rval += """
 - type: posix
@@ -44,9 +57,10 @@ def create_file_source_config_file_on(
     include_test_data_dir,
     required_role_expression,
     required_group_expression,
+    prefer_links: bool = False,
 ):
     file_contents = get_posix_file_source_config(
-        root_dir, required_role_expression, required_group_expression, include_test_data_dir
+        root_dir, required_role_expression, required_group_expression, include_test_data_dir, prefer_links=prefer_links
     )
     file_path = os.path.join(temp_dir, "file_sources_conf_posix.yml")
     with open(file_path, "w") as f:
@@ -67,6 +81,7 @@ def handle_galaxy_config_kwds(
         # Require role for access but do not require groups by default on every test to simplify them
         required_role_expression=REQUIRED_ROLE_EXPRESSION,
         required_group_expression="",
+        prefer_links: bool = False,
     ):
         temp_dir = os.path.realpath(mkdtemp())
         clazz_ = clazz_ or cls
@@ -79,6 +94,7 @@ def handle_galaxy_config_kwds(
             clazz_.include_test_data_dir,
             required_role_expression,
             required_group_expression,
+            prefer_links=prefer_links,
         )
         config["file_sources_config_file"] = file_sources_config_file
 
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index 42740dd72044..2d653ef04c4e 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -191,9 +191,9 @@ def test_rerun_deleted_dataset(self):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         assert (
             error_input1.text
-            == "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
+            == "Parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
         )
-        assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
+        assert error_col.text == "Parameter 'col': an invalid option ('3') was selected (valid options: 1)"
         # validate errors when inputs are missing
         self.components.tool_form.parameter_data_input_collection(parameter="input1").wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
@@ -201,8 +201,8 @@ def test_rerun_deleted_dataset(self):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         error_col_names = self.components.tool_form.parameter_error(parameter="col_names").wait_for_visible()
         assert error_input1.text == "Please provide a value for this option."
-        assert error_col.text == "parameter 'col': requires a value, but no legal values defined"
-        assert error_col_names.text == "parameter 'col_names': requires a value, but no legal values defined"
+        assert error_col.text == "Parameter 'col': requires a value, but no legal values defined"
+        assert error_col_names.text == "Parameter 'col_names': requires a value, but no legal values defined"
         # validate warnings when inputs are restored
         self.components.tool_form.parameter_data_input_single(parameter="input1").wait_for_and_click()
         self.sleep_for(self.wait_types.UX_TRANSITION)
@@ -210,9 +210,9 @@ def test_rerun_deleted_dataset(self):
         error_col = self.components.tool_form.parameter_error(parameter="col").wait_for_visible()
         assert (
             error_input1.text
-            == "parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
+            == "Parameter 'input1': the previously selected dataset has been deleted. Using default: ''."
         )
-        assert error_col.text == "parameter 'col': an invalid option ('3') was selected (valid options: 1)"
+        assert error_col.text == "Parameter 'col': an invalid option ('3') was selected (valid options: 1)"
 
     @selenium_test
     def test_rerun_dataset_collection_element(self):
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index ececfacac313..114e5101fcba 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -546,7 +546,7 @@ def test_editor_subworkflow_tool_upgrade_message(self):
         self.components.workflows.edit_button.wait_for_and_click()
         self.sleep_for(self.wait_types.UX_RENDER)
         self.assert_modal_has_text("Using version '0.2' instead of version '0.0.1'")
-        self.assert_modal_has_text("parameter 'inttest': an integer or workflow parameter is required")
+        self.assert_modal_has_text("Parameter 'inttest': an integer or workflow parameter is required")
         self.screenshot("workflow_editor_subworkflow_tool_upgrade")
         self.components.workflow_editor.modal_button_continue.wait_for_and_click()
         self.assert_workflow_has_changes_and_save()
diff --git a/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml b/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml
new file mode 100644
index 000000000000..090972695b10
--- /dev/null
+++ b/lib/tool_shed/test/test_data/repos/missing_data_ref/missing_data_ref.xml
@@ -0,0 +1,19 @@
+<tool id="missing_data_ref" name="missing_data_ref" version="1.0" profile="23.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        echo $column
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="column" type="data_column" />
+    </inputs>
+    <outputs>
+        <data name="output" format="text"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help/>
+</tool>
diff --git a/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml b/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml
new file mode 100644
index 000000000000..608dd7aad61c
--- /dev/null
+++ b/lib/tool_shed/test/test_data/repos/wrong_data_ref/wrong_data_ref.xml
@@ -0,0 +1,19 @@
+<tool id="wrong_data_ref" name="wrong_data_ref" version="1.0" profile="23.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        echo $column
+        ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="column" type="data_column" data_ref="nonsense" />
+    </inputs>
+    <outputs>
+        <data name="output" format="text"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help/>
+</tool>
diff --git a/pyproject.toml b/pyproject.toml
index 104425646e30..be857e903b7f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -149,7 +149,6 @@ dev = [
     "pytest-shard",
     "responses",
     "rucio-clients>=33.6.0 ; python_version>='3.9'",  # https://github.com/galaxyproject/galaxy/pull/17156
-    "scipy>=1.14.1; python_version>='3.10'",  # ase dependency, Python 3.13 support
     "selenium",
     "seletools",
     "Sphinx>=4.0",  # support docutils 0.17
@@ -238,6 +237,9 @@ keep-runtime-typing = true
 "lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]
 
 [tool.uv]
+constraint-dependencies = [
+    "scipy>=1.14.1; python_version>='3.10'",  # Python 3.13 support
+]
 default-groups = []
 extra-index-url = ["https://wheels.galaxyproject.org/simple"]
 index-strategy = "unsafe-best-match"
diff --git a/test/integration/test_remote_files_posix.py b/test/integration/test_remote_files_posix.py
index 7d588cdf9d25..75a449ff2e45 100644
--- a/test/integration/test_remote_files_posix.py
+++ b/test/integration/test_remote_files_posix.py
@@ -1,8 +1,8 @@
-# Before running this test, start nginx+webdav in Docker using following command:
-# docker run -v `pwd`/test/integration/webdav/data:/media  -e WEBDAV_USERNAME=alice -e WEBDAV_PASSWORD=secret1234 -p 7083:7083 jmchilton/webdavdev
-# Apache Docker host (shown next) doesn't work because displayname not set in response.
-# docker run -v `pwd`/test/integration/webdav:/var/lib/dav  -e AUTH_TYPE=Basic -e USERNAME=alice -e PASSWORD=secret1234  -e LOCATION=/ -p 7083:80 bytemark/webdav
+import os
 
+from sqlalchemy import select
+
+from galaxy.model import Dataset
 from galaxy_test.base import api_asserts
 from galaxy_test.base.populators import DatasetPopulator
 from galaxy_test.driver import integration_util
@@ -108,3 +108,53 @@ def _assert_list_response_matches_fixtures(self, list_response):
 
     def _assert_access_forbidden_response(self, response):
         api_asserts.assert_status_code_is(response, 403)
+
+
+class TestPreferLinksPosixFileSourceIntegration(PosixFileSourceSetup, integration_util.IntegrationTestCase):
+    dataset_populator: DatasetPopulator
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        PosixFileSourceSetup.handle_galaxy_config_kwds(
+            config,
+            cls,
+            prefer_links=True,
+        )
+
+    def setUp(self):
+        super().setUp()
+        self._write_file_fixtures()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    def test_links_by_default(self):
+        with self.dataset_populator.test_history() as history_id:
+            element = dict(src="url", url="gxfiles://linking_source/a")
+            target = {
+                "destination": {"type": "hdas"},
+                "elements": [element],
+            }
+            targets = [target]
+            payload = {
+                "history_id": history_id,
+                "targets": targets,
+            }
+            new_dataset = self.dataset_populator.fetch(payload, assert_ok=True).json()["outputs"][0]
+            content = self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset)
+            assert content == "a\n", content
+            stmt = select(Dataset).order_by(Dataset.create_time.desc()).limit(1)
+            dataset = self._app.model.session.execute(stmt).unique().scalar_one()
+            assert dataset.external_filename.endswith("/root/a")
+            assert os.path.exists(dataset.external_filename)
+            assert open(dataset.external_filename).read() == "a\n"
+            payload = self.dataset_populator.run_tool(
+                tool_id="cat",
+                inputs={
+                    "input1": {"src": "hda", "id": new_dataset["id"]},
+                },
+                history_id=history_id,
+            )
+            derived_dataset = payload["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            derived_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=derived_dataset)
+            assert derived_content.strip() == "a"
diff --git a/test/unit/app/tools/test_parameter_validation.py b/test/unit/app/tools/test_parameter_validation.py
index 4b69034fac4b..d2022c4cba42 100644
--- a/test/unit/app/tools/test_parameter_validation.py
+++ b/test/unit/app/tools/test_parameter_validation.py
@@ -85,7 +85,7 @@ def test_NoOptionsValidator(self):
 </param>"""
         )
         p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter index: No options available for selection"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'index': No options available for selection"):
             p.validate(None)
 
         p = self._parameter_for(
@@ -95,7 +95,7 @@ def test_NoOptionsValidator(self):
     <validator type="no_options" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter index: Options available for selection"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'index': Options available for selection"):
             p.validate("foo")
         p.validate(None)
 
@@ -107,7 +107,7 @@ def test_EmptyTextfieldValidator(self):
 </param>"""
         )
         p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Field requires a value"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field requires a value"):
             p.validate("")
 
         p = self._parameter_for(
@@ -116,7 +116,7 @@ def test_EmptyTextfieldValidator(self):
     <validator type="empty_field" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Field must not set a value"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Field must not set a value"):
             p.validate("foo")
         p.validate("")
 
@@ -130,14 +130,14 @@ def test_RegexValidator(self):
         p.validate("Foo")
         p.validate("foo")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Fop' does not match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Fop' does not match regular expression '\[Ff\]oo'"
         ):
             p.validate("Fop")
 
         # test also valitation of lists (for select parameters)
         p.validate(["Foo", "foo"])
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Fop' does not match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Fop' does not match regular expression '\[Ff\]oo'"
         ):
             p.validate(["Foo", "Fop"])
 
@@ -148,16 +148,16 @@ def test_RegexValidator(self):
 </param>"""
         )
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'Foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'Foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate("Foo")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate("foo")
         p.validate("Fop")
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value 'foo' does match regular expression '\[Ff\]oo'"
+            ValueError, r"Parameter 'blah': Value 'foo' does match regular expression '\[Ff\]oo'"
         ):
             p.validate(["Fop", "foo"])
         p.validate(["Fop", "fop"])
@@ -171,9 +171,9 @@ def test_LengthValidator(self):
         )
         p.validate("foo")
         p.validate("bar")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
             p.validate("f")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must have length of at least 2 and at most 8"):
             p.validate("foobarbaz")
 
         p = self._parameter_for(
@@ -182,9 +182,9 @@ def test_LengthValidator(self):
     <validator type="length" min="2" max="8" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must not have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("foo")
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Must not have length of at least 2 and at most 8"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Must not have length of at least 2 and at most 8"):
             p.validate("bar")
         p.validate("f")
         p.validate("foobarbaz")
@@ -204,11 +204,11 @@ def test_InRangeValidator(self):
     <validator type="in_range" message="Doh!! %s not in range" min="10" exclude_min="true" max="20"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Doh!! 10 not in range"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 10 not in range"):
             p.validate(10)
         p.validate(15)
         p.validate(20)
-        with self.assertRaisesRegex(ValueError, "Parameter blah: Doh!! 21 not in range"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': Doh!! 21 not in range"):
             p.validate(21)
 
         p = self._parameter_for(
@@ -220,12 +220,12 @@ def test_InRangeValidator(self):
         p.validate(10)
         with self.assertRaisesRegex(
             ValueError,
-            r"Parameter blah: Value \('15'\) must not fulfill \(10 < value <= 20\)",
+            r"Parameter 'blah': Value \('15'\) must not fulfill \(10 < value <= 20\)",
         ):
             p.validate(15)
         with self.assertRaisesRegex(
             ValueError,
-            r"Parameter blah: Value \('20'\) must not fulfill \(10 < value <= 20\)",
+            r"Parameter 'blah': Value \('20'\) must not fulfill \(10 < value <= 20\)",
         ):
             p.validate(20)
         p.validate(21)
@@ -253,7 +253,7 @@ def test_DatasetOkValidator(self):
         p.validate(ok_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset is still being generated, select another dataset or wait until it is completed",
+            "Parameter 'blah': The selected dataset is still being generated, select another dataset or wait until it is completed",
         ):
             p.validate(notok_hda)
         p = self._parameter_for(
@@ -262,7 +262,7 @@ def test_DatasetOkValidator(self):
     <validator type="dataset_ok_validator" negate="true"/>
 </param>"""
         )
-        with self.assertRaisesRegex(ValueError, "Parameter blah: The selected dataset must not be in state OK"):
+        with self.assertRaisesRegex(ValueError, "Parameter 'blah': The selected dataset must not be in state OK"):
             p.validate(ok_hda)
         p.validate(notok_hda)
 
@@ -288,7 +288,7 @@ def test_DatasetEmptyValidator(self):
         )
         p.validate(full_hda)
         with self.assertRaisesRegex(
-            ValueError, "Parameter blah: The selected dataset is empty, this tool expects non-empty files."
+            ValueError, "Parameter 'blah': The selected dataset is empty, this tool expects non-empty files."
         ):
             p.validate(empty_hda)
 
@@ -299,7 +299,7 @@ def test_DatasetEmptyValidator(self):
 </param>"""
         )
         with self.assertRaisesRegex(
-            ValueError, "Parameter blah: The selected dataset is non-empty, this tool expects empty files."
+            ValueError, "Parameter 'blah': The selected dataset is non-empty, this tool expects empty files."
         ):
             p.validate(full_hda)
         p.validate(empty_hda)
@@ -329,7 +329,7 @@ def test_DatasetExtraFilesPathEmptyValidator(self):
         p.validate(has_extra_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input.",
+            "Parameter 'blah': The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input.",
         ):
             p.validate(has_no_extra_hda)
 
@@ -342,7 +342,7 @@ def test_DatasetExtraFilesPathEmptyValidator(self):
 
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: The selected dataset's extra_files_path directory is non-empty or does exist, this tool expects empty extra_files_path directories associated with the selected input.",
+            "Parameter 'blah': The selected dataset's extra_files_path directory is non-empty or does exist, this tool expects empty extra_files_path directories associated with the selected input.",
         ):
             p.validate(has_extra_hda)
         p.validate(has_no_extra_hda)
@@ -376,7 +376,7 @@ def test_MetadataValidator(self):
         p = self._parameter_for(xml=param_xml.format(check="strandCol", skip=""))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -385,7 +385,7 @@ def test_MetadataValidator(self):
         p = self._parameter_for(xml=param_xml.format(check="", skip="dbkey,comment_lines,column_names,nameCol"))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -398,7 +398,7 @@ def test_MetadataValidator(self):
         p = self._parameter_for(xml=param_xml_negate.format(check="nameCol", skip=""))
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: At least one of the checked metadata 'nameCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': At least one of the checked metadata 'nameCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -409,7 +409,7 @@ def test_MetadataValidator(self):
         )
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
+            "Parameter 'blah': At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes",
         ):
             p.validate(hda)
 
@@ -437,7 +437,7 @@ def test_UnspecifiedBuildValidator(self):
         p.validate(has_dbkey_hda)
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Unspecified genome build, click the pencil icon in the history item to set the genome build",
+            "Parameter 'blah': Unspecified genome build, click the pencil icon in the history item to set the genome build",
         ):
             p.validate(has_no_dbkey_hda)
 
@@ -449,7 +449,7 @@ def test_UnspecifiedBuildValidator(self):
         )
         with self.assertRaisesRegex(
             ValueError,
-            "Parameter blah: Specified genome build, click the pencil icon in the history item to remove the genome build",
+            "Parameter 'blah': Specified genome build, click the pencil icon in the history item to remove the genome build",
         ):
             p.validate(has_dbkey_hda)
         p.validate(has_no_dbkey_hda)
diff --git a/test/unit/data/datatypes/test_constructive_solid_geometry.py b/test/unit/data/datatypes/test_constructive_solid_geometry.py
new file mode 100644
index 000000000000..bfaa95ed804d
--- /dev/null
+++ b/test/unit/data/datatypes/test_constructive_solid_geometry.py
@@ -0,0 +1,16 @@
+from galaxy.datatypes.constructive_solid_geometry import VtkXml
+from .util import (
+    get_dataset,
+    MockDatasetDataset,
+)
+
+
+def test_vtkXml_set_meta():
+    vtkXml = VtkXml()
+    with get_dataset("data.vtu") as dataset:
+        dataset.dataset = MockDatasetDataset(dataset.get_file_name())
+        vtkXml.set_meta(dataset)
+
+    assert dataset.metadata.vtk_version == "0.1"
+    assert dataset.metadata.file_format == "XML"
+    assert dataset.metadata.dataset_type == "UnstructuredGrid"
diff --git a/test/unit/tool_shed/test_tool_validation.py b/test/unit/tool_shed/test_tool_validation.py
index a1f421120ecc..cf538e5599a1 100644
--- a/test/unit/tool_shed/test_tool_validation.py
+++ b/test/unit/tool_shed/test_tool_validation.py
@@ -11,6 +11,8 @@
 BOWTIE2_INDICES = os.path.join(
     galaxy_directory(), "lib/tool_shed/test/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample"
 )
+MISSING_DATA_REF_DIR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/repos/missing_data_ref")
+WRONG_DATA_REF_DIR = os.path.join(galaxy_directory(), "lib/tool_shed/test/test_data/repos/wrong_data_ref")
 
 
 def test_validate_valid_tool():
@@ -64,6 +66,22 @@ def test_validate_tool_without_index():
         assert not tool.params_with_missing_index_file
 
 
+def test_validate_missing_data_ref():
+    repo_dir = MISSING_DATA_REF_DIR
+    with get_tool_validator() as tv:
+        full_path = os.path.join(repo_dir, "missing_data_ref.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
+        assert valid is False
+
+
+def test_validate_wrong_data_ref():
+    repo_dir = WRONG_DATA_REF_DIR
+    with get_tool_validator() as tv:
+        full_path = os.path.join(repo_dir, "wrong_data_ref.xml")
+        tool, valid, message = tv.load_tool_from_config(repository_id=None, full_path=full_path)
+        assert valid is False
+
+
 @contextmanager
 def get_tool_validator():
     app = MockApp()
diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
new file mode 100644
index 000000000000..8f52af0b7b7b
--- /dev/null
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -0,0 +1,107 @@
+<tool id="interactive_tool_ilastik" tool_type="interactive" name="Ilastik" version="@VERSION@" profile="23.0">
+    <description>interactive learning and segmentation toolkit</description>
+    <macros>
+        <token name="@VERSION@">1.4.0</token>
+    </macros>
+    <requirements>
+        <container type="docker">quay.io/galaxy/ilastik:@VERSION@</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Ilastik" requires_domain="True">
+            <port>5800</port>
+        </entry_point>
+    </entry_points>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        ## Check inputs have no duplicated element_identifier:
+        #set labels = [input.element_identifier for input in $infiles]
+        #set duplicates = [label for label in labels if labels.count(label) > 1]
+        #if len(duplicates) > 0:
+            #set unique_duplicates = list(set(duplicates))
+            echo "Cannot run ilastik because these identifiers are present more than once:" &&
+            #for label in $unique_duplicates:
+                echo $label &&
+            #end for
+            exit 1 &&
+        #end if
+        export HOME=\$PWD &&
+        ## Create a directory where the app user has access
+        mkdir -p ./output &&
+        chown 1000:1000 ./output/ &&
+        ## Make a copy of the existing project if exists
+        #if str($input_type.existing) == "existing":
+            cp '$input_type.project' ./output/MyProject.ilp &&
+        #end if
+
+        ## Link input images to current working directory
+        #for input in $infiles:
+            ln -s '$input' ./'$input.element_identifier'.tif &&
+        #end for
+        ## Write the bash script to run:
+        #if str($input_type.existing) == "new":
+            echo "ilastik --new_project \$HOME/output/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
+        #else:
+            echo "ilastik --project \$HOME/output/MyProject.ilp" > ./ilastik_with_args &&
+        #end if
+        ## Copy it to /bin/ so it will be used by the container:
+        chmod +x ./ilastik_with_args &&
+        cp ./ilastik_with_args '/bin/' &&
+        /init
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="existing" type="select" label="Which project you want to work on?">
+                <option value="new">Start a new project</option>
+                <option value="existing">Modify an existing project</option>
+            </param>
+            <when value="new">
+                <param name="Workflow" type="select" label="Type of Workflow" >
+                    <option value="PixelClassificationWorkflow">Pixel Classification</option>
+                    <option value="AutocontextTwoStage">Autocontext (2-stage)</option>
+                    <option value="ObjectClassificationWorkflowPixel">Pixel Classification + Object Classification</option>
+                    <option value="ObjectClassificationWorkflowPrediction">Object Classification [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="ObjectClassificationWorkflowBinary">Object Classification [Inputs: Raw Data, Segmentation]</option>
+                    <option value="ConservationTrackingWorkflowFromBinary">Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="ConservationTrackingWorkflowFromPrediction">Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromBinary">Animal Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromPrediction">Animal Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="StructuredTrackingWorkflowFromBinary">Tracking with Learning [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="StructuredTrackingWorkflowFromPrediction">Tracking with Learning [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="EdgeTrainingWithMulticutWorkflow">Bounary-based Segmentation with Multicut</option>
+                    <option value="CountingWorkflow">Cell Density Counting</option>
+                    <option value="DataConversionWorkflow">Data Conversion</option>
+                    <option value="neuralNetwork.RemoteWorkflow">Neural Network Classification (Remote)</option>
+                    <option value="neuralNetwork.LocalWorkflow">Neural Network Classification (Local)</option>
+                </param>
+            </when>
+            <when value="existing">
+                <param argument="--project" type="data" format="h5" label="Existing ilastik project" />
+            </when>
+        </conditional>
+        <param name="infiles" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/>
+    </inputs>
+    
+    <outputs>
+        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="output/MyProject.ilp"/>
+    </outputs>
+    
+    <tests>
+    </tests>
+    
+    <help><![CDATA[
+        Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.
+
+        This tool has been designed uniquely to make/modify a project.
+        
+        - It requires that input images have unique identifiers.
+        - When you have trained your project, save it and quit the application. The project called 'MyProject.ilp' will be imported into your history.
+        - If you want to modify a project, make sure you use at least the same images (with the same identifiers) as the first time (but you can add more).
+
+        Please, check the documentation at https://www.ilastik.org/documentation/.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41592-019-0582-9</citation>
+    </citations>
+</tool>