diff --git a/workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md
index 886170a1e9..2abdb92bec 100644
--- a/workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md
+++ b/workflows/amplicon/qiime2/qiime2-I-import/CHANGELOG.md
@@ -1,5 +1,19 @@
 # Changelog
 
+## [0.3] 2024-09-23
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.5.0+q2galaxy.2024.5.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.5.0+q2galaxy.2024.5.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0`
+- `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0`
+
 ## [0.1] 2024-04-08
 First release.
 ## [0.2] 2024-05-23
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
index 1dad6979a7..bfe453f662 100644
--- a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.2",
+    "release": "0.3",
     "name": "QIIME2 Ia: multiplexed data (single-end)",
     "steps": {
         "0": {
@@ -80,7 +80,7 @@
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "A tab separated metadata file",
+                    "description": "Metadata",
                     "name": "Metadata"
                 }
             ],
@@ -134,7 +134,7 @@
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "If reverse complement of barcodes is necessary for the analysis, choose Yes.",
+                    "description": "Reverse complement barcodes",
                     "name": "Reverse complement barcodes"
                 }
             ],
@@ -155,7 +155,7 @@
         },
         "5": {
             "annotation": "qiime2 tools input\nThis step allows the input of the files to be analysed and then generate a qza output, necessary for the QIIME2 pipeline.",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "errors": null,
             "id": 5,
             "input_connections": {
@@ -195,15 +195,15 @@
                     "output_name": "imported_data"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "tool_shed_repository": {
-                "changeset_revision": "10447a4b0cc3",
+                "changeset_revision": "f9e68fa06585",
                 "name": "qiime2_core__tools__import",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"import_root\": {\"type\": \"EMPSingleEndSequences\", \"__current_case__\": 5, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPSingleEndDirFmt\", \"__current_case__\": 1, \"import_sequences\": {\"name\": \"sequences.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+dist.h193f7cc9.3",
+            "tool_state": "{\"import_root\": {\"type\": \"EMPSingleEndSequences\", \"__current_case__\": 7, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPSingleEndDirFmt\", \"__current_case__\": 1, \"import_sequences\": {\"name\": \"sequences.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2024.5.0+dist.he540b0b0",
             "type": "tool",
             "uuid": "b39f05da-9f23-47ff-9695-b21bb61f18a2",
             "when": null,
@@ -211,7 +211,7 @@
         },
         "6": {
             "annotation": "Import the metadata as artifact",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -247,15 +247,15 @@
                     "output_name": "imported_data"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "tool_shed_repository": {
-                "changeset_revision": "10447a4b0cc3",
+                "changeset_revision": "f9e68fa06585",
                 "name": "qiime2_core__tools__import",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 29, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+dist.h193f7cc9.3",
+            "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 48, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2024.5.0+dist.he540b0b0",
             "type": "tool",
             "uuid": "9caaabce-3a1a-4bf9-9fa0-d6fbe24a4bb4",
             "when": null,
@@ -263,7 +263,7 @@
         },
         "7": {
             "annotation": "qiime2 demux emp-single\nDemultiplex sequence data generated with the EMP protocol.",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.5.0+q2galaxy.2024.5.0",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -284,7 +284,20 @@
                     "output_name": "imported_data"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-single",
+                    "name": "__q2galaxy__GUI__section__extra_opts__"
+                },
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-single",
+                    "name": "barcodes"
+                },
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-single",
+                    "name": "barcodes"
+                }
+            ],
             "label": "Demultiplex single-end data",
             "name": "qiime2 demux emp-single",
             "outputs": [
@@ -322,15 +335,15 @@
                     "output_name": "per_sample_sequences"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2023.5.0+q2galaxy.2023.5.0.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_single/qiime2__demux__emp_single/2024.5.0+q2galaxy.2024.5.0",
             "tool_shed_repository": {
-                "changeset_revision": "75b07a996ac0",
+                "changeset_revision": "19e2495b60e8",
                 "name": "qiime2__demux__emp_single",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"golay_error_correction\": true, \"rev_comp_barcodes\": false, \"rev_comp_mapping_barcodes\": {\"__class__\": \"ConnectedValue\"}, \"ignore_description_mismatch\": false}, \"barcodes\": {\"type\": \"qza\", \"__current_case__\": 1, \"source\": {\"__class__\": \"ConnectedValue\"}, \"column\": {\"__class__\": \"ConnectedValue\"}}, \"seqs\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+            "tool_version": "2024.5.0+q2galaxy.2024.5.0",
             "type": "tool",
             "uuid": "23dd9199-b8aa-4daf-893f-1ca504ee0292",
             "when": null,
@@ -344,7 +357,7 @@
         },
         "8": {
             "annotation": "qiime2 demux summarize\nSummarize counts per sample.\n(Galaxy Version 2023.5.0+q2galaxy.2023.5.0.2)",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -375,15 +388,15 @@
                     "output_name": "visualization"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2023.5.0+q2galaxy.2023.5.0.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__summarize/qiime2__demux__summarize/2024.5.0+q2galaxy.2024.5.0",
             "tool_shed_repository": {
-                "changeset_revision": "d8a9f74f1a6d",
+                "changeset_revision": "acb0f8837379",
                 "name": "qiime2__demux__summarize",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"__q2galaxy__GUI__section__extra_opts__\": {\"n\": \"10000\"}, \"data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+q2galaxy.2023.5.0.2",
+            "tool_version": "2024.5.0+q2galaxy.2024.5.0",
             "type": "tool",
             "uuid": "3b70c32e-3cd7-4444-b5e8-3ecf0916a14f",
             "when": null,
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga
index 08397c88de..92661c3da4 100644
--- a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga
@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.2",
+    "release": "0.3",
     "name": "QIIME2 Ib: multiplexed data (paired-end)",
     "steps": {
         "0": {
@@ -182,7 +182,7 @@
         },
         "6": {
             "annotation": "qiime2 tools import\nImport data into a QIIME 2 artifact",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -226,15 +226,15 @@
                     "output_name": "imported_data"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "tool_shed_repository": {
-                "changeset_revision": "10447a4b0cc3",
+                "changeset_revision": "f9e68fa06585",
                 "name": "qiime2_core__tools__import",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"import_root\": {\"type\": \"EMPPairedEndSequences\", \"__current_case__\": 4, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPPairedEndDirFmt\", \"__current_case__\": 1, \"import_forward\": {\"name\": \"forward.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_reverse\": {\"name\": \"reverse.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+dist.h193f7cc9.3",
+            "tool_state": "{\"import_root\": {\"type\": \"EMPPairedEndSequences\", \"__current_case__\": 6, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"EMPPairedEndDirFmt\", \"__current_case__\": 1, \"import_forward\": {\"name\": \"forward.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_reverse\": {\"name\": \"reverse.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}, \"import_barcodes\": {\"name\": \"barcodes.fastq.gz\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2024.5.0+dist.he540b0b0",
             "type": "tool",
             "uuid": "6a264e2d-ac11-498f-bdcf-c115221bbc91",
             "when": null,
@@ -242,7 +242,7 @@
         },
         "7": {
             "annotation": "Import metadata into a QIIME 2 artifact",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -278,15 +278,15 @@
                     "output_name": "imported_data"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2_core__tools__import/qiime2_core__tools__import/2024.5.0+dist.he540b0b0",
             "tool_shed_repository": {
-                "changeset_revision": "10447a4b0cc3",
+                "changeset_revision": "f9e68fa06585",
                 "name": "qiime2_core__tools__import",
                 "owner": "q2d2",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 29, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2023.5.0+dist.h193f7cc9.3",
+            "tool_state": "{\"import_root\": {\"type\": \"ImmutableMetadata\", \"__current_case__\": 48, \"__q2galaxy__GUI__cond__format__\": {\"format\": \"ImmutableMetadataFormat\", \"__current_case__\": 0, \"import\": {\"name\": \"__q2galaxy__::literal::None\", \"data\": {\"__class__\": \"ConnectedValue\"}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2024.5.0+dist.he540b0b0",
             "type": "tool",
             "uuid": "b2974890-9277-4369-81af-4fa0ff80c5fe",
             "when": null,
@@ -294,7 +294,7 @@
         },
         "8": {
             "annotation": "qiime2 demux emp-paired\nDemultiplex paired-end sequence data generated with the EMP protocol.",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.5.0+q2galaxy.2024.5.0",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -315,7 +315,20 @@
                     "output_name": "imported_data"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-paired",
+                    "name": "__q2galaxy__GUI__section__extra_opts__"
+                },
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-paired",
+                    "name": "barcodes"
+                },
+                {
+                    "description": "runtime parameter for tool qiime2 demux emp-paired",
+                    "name": "barcodes"
+                }
+            ],
             "label": "Demultiplex paired-end sequences",
             "name": "qiime2 demux emp-paired",
             "outputs": [
@@ -353,15 +366,15 @@
                     "output_name": "per_sample_sequences"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2024.5.0+q2galaxy.2024.5.0",
             "tool_shed_repository": {
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@@ -375,7 +388,7 @@
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@@ -406,15 +419,15 @@
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