Change tool versions in ToolDistillator parameters (#522)

galaxyproject · Sep 19, 2024 · 7907910 · 7907910
1 parent e1b2f11
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diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.1.4] 2024-09-19
+
+### Manual update
+
+- Updated the tool versions manually in the ToolDistillator parameters
+
 ## [1.1.3] 2024-09-09
 
 ### Automatic update

diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga
@@ -27,7 +27,7 @@
     ],
     "format-version": "0.1",
     "license": "GPL-3.0-or-later",
-    "release": "1.1.3",
+    "release": "1.1.4",
     "name": "bacterial_genome_annotation",
     "steps": {
         "0": {
@@ -1127,7 +1127,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.6\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.7.2.3\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.0.2\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.9.3\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"plasmidfinder\", \"__current_case__\": 14, \"input\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_result_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"genome_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmid_hit_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.6\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"isescan\", \"__current_case__\": 11, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"orf_faa_path\": {\"__class__\": \"ConnectedValue\"}, \"is_fna_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.7.2.3\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"integronfinder2\", \"__current_case__\": 10, \"input\": {\"__class__\": \"ConnectedValue\"}, \"summary_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.0.5\", \"reference_database_version\": null}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"bakta\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"annotation_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_genbank_path\": {\"__class__\": \"ConnectedValue\"}, \"annotation_embl_path\": {\"__class__\": \"ConnectedValue\"}, \"contig_sequences_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_protein_path\": {\"__class__\": \"ConnectedValue\"}, \"hypothetical_tabular_path\": {\"__class__\": \"ConnectedValue\"}, \"plot_file_path\": {\"__class__\": \"ConnectedValue\"}, \"summary_result_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"amino_acid_annotation_path\": {\"__class__\": \"ConnectedValue\"}, \"gff_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.9.4\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "0.9+galaxy0",
             "type": "tool",
             "uuid": "678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6",