PathoGFAIR: fasttree 2.1.10+galaxy1 -> +galaxy3, plus test schema regularization

fasttree 2.1.10+galaxy1 is no longer installable from the toolshed (only
2.1.10 and 2.1.10+galaxy3 are), so the workflow could not be invoked and
lint errored. Supersedes galaxyproject#1162, which bumped content_id/tool_id/changeset
but left tool_version at +galaxy1 in all three fasttree steps.

Also carries the class:Collection / collection_type test annotations for
this workflow, split out of galaxyproject#1286.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: jmchilton

workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.1] - 2026-07-14
+
+### Changed
+- Update fasttree from 2.1.10+galaxy1 to 2.1.10+galaxy3
+
 ## [0.1] - 2024-04-24
 
 First release.

workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation-tests.yml

@@ -111,6 +111,7 @@
     metadata:
   outputs:
     adjusted_abricate_vfs_tabular_part1:
+      class: Collection
       attributes: {}
       element_tests:
         YP_001006764:

workflows/microbiome/pathogen-identification/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation.ga

@@ -202,7 +202,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1",
+    "release": "0.1.1",
     "name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
     "report": {
         "markdown": "# Pathogen Detection - PathoGFAIR Samples Aggregation and Visualisation Workflow Report\nBelow are the results for the PathoGFAIR Samples Aggregation and Visualisation Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nTabular files and a FASTA file from the Gene-based Pathogen Identification workflow, four other tabular files from Nanopore Preprocessing and Nanopore - Allele-based Pathogen Identification workflow, and an optional Metadata tabular file with more sample information:\n\nFrom Gene-based Pathogenic Identification workflow: \n- contigs, FASTA file\n- VFs, Tabular file\n- vfs_of_genes_identified_by_vfdb, Tabular file\n- AMRs, Tabular file\n- amr_identified_by_ncbi, Tabular file\n\nFrom Nanopore - Allele bases Pathogen Identification workflow: \n- number_of_variants_per_sample, Tabular file\n- mapping_mean_depth_per_sample, Tabular file\n- mapping_coverage_percentage_per_sample, Tabular file\n\nFrom Nanopore Preprocessing: \n- removed_hosts_percentage_tabular, Tabular file\n\n## Some of the Workflow Outputs\n\n1- All Samples VFs Heatmap\n\n```galaxy\nhistory_dataset_as_image(output=\"heatmap_png\")\n```\n\n2- All samples phylogenetic tree VFs based\n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_vfs\")\n```\n\n3- All samples Phylogenetic tree AMR based \n\n```galaxy\nhistory_dataset_as_image(output=\"all_samples_phylogenetic_tree_based_amrs\")\n```\n\n4- Bar-plot for the Number of reads before host sequences removal and Number of found host reads per sample, performed in the Nanopore - Preprocessing workflow\n\n\n5- Barplot for the total number of removed host sequences per sample\n\n \n6- Barplot for the Mapping mean depth of coverage per sample\n\n\n6- Barplot for the Mapping breadth of coverage percentage per sample\n\n\n7- Barplot for the total number of complex variants and SNPs identified per sample\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"
@@ -2402,7 +2402,7 @@
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         "55": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "errors": null,
             "id": 55,
             "input_connections": {
@@ -2438,15 +2438,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "e005e659ae21",
+                "changeset_revision": "bc939965ce41",
                 "name": "fasttree",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced_selector\": {\"maximize\": \"min\", \"__current_case__\": 0}, \"input_selector\": {\"select_format\": \"fasta\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"quote\": false, \"intree_selector\": {\"intree_format\": \"none\", \"__current_case__\": 0}}, \"model_selector\": {\"format\": \"-nt\", \"__current_case__\": 0, \"model\": \"-gtr\"}, \"save_logfile\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.1.10+galaxy1",
+            "tool_version": "2.1.10+galaxy3",
             "type": "tool",
             "uuid": "4faa1735-bea7-4e71-9961-9928bbba13d3",
             "when": null,
@@ -2871,7 +2871,7 @@
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         "66": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "errors": null,
             "id": 66,
             "input_connections": {
@@ -2899,23 +2899,23 @@
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             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "e005e659ae21",
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                 "name": "fasttree",
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-            "tool_version": "2.1.10+galaxy1",
+            "tool_version": "2.1.10+galaxy3",
             "type": "tool",
             "uuid": "38119133-c15d-472e-9df2-38ea8519f795",
             "when": null,
             "workflow_outputs": []
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         "67": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "errors": null,
             "id": 67,
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@@ -2943,15 +2943,15 @@
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             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "e005e659ae21",
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                 "name": "fasttree",
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-            "tool_version": "2.1.10+galaxy1",
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