Updating workflows/bacterial_genomics/amr_gene_detection from 1.1.6 to 1.1.7

Author: planemo-autoupdate

workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [1.1.7] - 2025-11-03
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.1+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.3+galaxy0`
+
 ## [1.1.6] 2025-06-18
 
 ### Manual update

workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga

@@ -194,7 +194,7 @@
         },
         "6": {
             "annotation": "staramr_amr_genes",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.1+galaxy0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -389,15 +389,15 @@
                     "output_name": "summary"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.1+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "6d5c8a6ceea0",
+                "changeset_revision": "eaa563bd535a",
                 "name": "staramr",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced\": {\"pid_threshold\": \"90.0\", \"percent_length_overlap_resfinder\": \"60.0\", \"percent_length_overlap_pointfinder\": \"95.0\", \"percent_length_overlap_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations_file\": {\"__class__\": \"RuntimeValue\"}, \"plasmidfinder_type\": \"include_all\"}, \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"hide_db_build\": \"\", \"output_files\": {\"output_selection\": [\"mlst_table\", \"summary_table\", \"detailed_summary_table\", \"resfinder_table\", \"plasmidfinder_table\", \"pointfinder_table\", \"settings_output\", \"excel_output\"]}, \"pointfinder_organism\": {\"__class__\": \"ConnectedValue\"}, \"staramr_db_select\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.11.0+galaxy3",
+            "tool_version": "0.11.1+galaxy0",
             "type": "tool",
             "uuid": "ed320061-0b9d-4fcd-bec2-02388d18b84c",
             "when": null,
@@ -618,7 +618,7 @@
         },
         "9": {
             "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.3+galaxy0",
             "errors": null,
             "id": 9,
             "input_connections": {
@@ -700,15 +700,15 @@
                     "output_name": "output_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "c6b5c2975e51",
+                "changeset_revision": "a5ef8d31c40e",
                 "name": "tooldistillator",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"abricate\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"staramr\", \"__current_case__\": 37, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mlst_file_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmidfinder_file_path\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_file_path\": {\"__class__\": \"ConnectedValue\"}, \"setting_file_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"amrfinderplus\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"point_mutation_report_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_sequence_path\": {\"__class__\": \"ConnectedValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.0.0+galaxy1",
+            "tool_version": "1.0.3+galaxy0",
             "type": "tool",
             "uuid": "1589f8a1-65b6-43f0-9e75-cad9b1752e5c",
             "when": null,
@@ -722,7 +722,7 @@
         },
         "10": {
             "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.3+galaxy0",
             "errors": null,
             "id": 10,
             "input_connections": {
@@ -760,15 +760,15 @@
                     "output_name": "summary_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "3d0223265277",
+                "changeset_revision": "a4506449c300",
                 "name": "tooldistillator_summarize",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"summarize_data\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.0.0+galaxy1",
+            "tool_version": "1.0.3+galaxy0",
             "type": "tool",
             "uuid": "a88f6b82-502c-46cf-a174-2c8361e8e8dd",
             "when": null,
@@ -792,7 +792,7 @@
         "AMR",
         "AMR-detection"
     ],
-    "uuid": "284cc748-7532-4749-8f68-d19d41c048ef",
+    "uuid": "c227dc2b-3661-46f7-8fee-88728d05ef3f",
     "version": 1,
-    "release": "1.1.6"
+    "release": "1.1.7"
 }