changed worrding for BUSCO selector

workflow4metabolomics · Nov 7, 2023 · 46d8534 · 46d8534
1 parent d3ae7da
commit 46d8534
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diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Changed parameters of gfastats for postprocessing of contigs generated with purge_dups. Specfically:
   - "Terminal overlap selection" is set to "Yes"
   - "Generated the initial set of paths" is set to "No"
+- Made BUSCO lineage selectable from workflow launch interface
 
 
 ## [0.1.1] - 2023-11-01

diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga
@@ -14,8 +14,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release":"0.2.0",
-    "name": "Purge duplicate contigs (WF6)",
+    "name": "Purge duplicate contigs (WF6) (imported from uploaded file)",
     "steps": {
         "0": {
             "annotation": "",
@@ -33,7 +32,7 @@
             "name": "Input dataset collection",
             "outputs": [],
             "position": {
-                "left": 0.0,
+                "left": 0,
                 "top": 0
             },
             "tool_id": null,
@@ -188,15 +187,15 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "Busco Lineage"
+                    "name": "Provide lineage for BUSCO (e.g., Vertebrata)"
                 }
             ],
-            "label": "Busco Lineage",
+            "label": "Provide lineage for BUSCO (e.g., Vertebrata)",
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 254.36771647135419,
-                "top": 666.2375081380211
+                "left": 216.76248168945312,
+                "top": 631.0250244140625
             },
             "tool_id": null,
             "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
@@ -1125,16 +1124,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool gfastats",
-                    "name": "input_file"
-                },
-                {
-                    "description": "runtime parameter for tool gfastats",
-                    "name": "mode_condition"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "gfastats",
             "outputs": [
@@ -1163,7 +1153,7 @@
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.3.6+galaxy0",
             "type": "tool",
             "uuid": "55a89d15-73d3-4e8b-b9da-06e650bd00cf",
@@ -2362,16 +2352,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool gfastats",
-                    "name": "input_file"
-                },
-                {
-                    "description": "runtime parameter for tool gfastats",
-                    "name": "mode_condition"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "gfastats",
             "outputs": [
@@ -2381,8 +2362,8 @@
                 }
             ],
             "position": {
-                "left": 5039.509429931641,
-                "top": 1348.9124755859375
+                "left": 5040.299957275391,
+                "top": 1348.9125366210938
             },
             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -2400,7 +2381,7 @@
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.3.6+galaxy0",
             "type": "tool",
             "uuid": "f15eb7b7-c881-490b-8734-cc4d934eaa3a",
@@ -3441,6 +3422,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "f37b87cb-969b-4464-b256-47d904ae8955",
-    "version": 3
+    "uuid": "84966ef2-7c02-4b71-92bc-6c63feddd4ef",
+    "version": 1
 }