Updating workflows/microbiome/metagenomic-genes-catalogue from 1.1 to 1.2

Author: planemo-autoupdate

workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.2] - 2025-12-10
+
+### 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/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1`
+
 ## [1.1] - 2025-12-08
 
 ### Automatic update

workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue.ga

@@ -879,7 +879,7 @@
         },
         "14": {
             "annotation": "",
-            "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": 14,
             "input_connections": {
@@ -981,15 +981,15 @@
                     "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\": \"98.0\", \"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\"]}, \"pointfinder_organism\": \"disabled\", \"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": "bb337b49-0c9f-44bb-bf1b-aab2bee83423",
             "when": null,
@@ -1383,7 +1383,7 @@
         },
         "20": {
             "annotation": "Rename dynamic column 2",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1",
             "errors": null,
             "id": 20,
             "input_connections": {
@@ -1414,15 +1414,15 @@
                     "output_name": "output_dataset"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "3f54cd56a65e",
+                "changeset_revision": "8537763e4713",
                 "name": "table_pandas_rename_column",
                 "owner": "recetox",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"columns_selection\": [{\"__index__\": 0, \"column\": \"2\", \"new_name\": \"Coverage\"}], \"input_dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.2.3+galaxy0",
+            "tool_version": "2.2.3+galaxy1",
             "type": "tool",
             "uuid": "691a5e64-dce3-477b-aa35-f519a9b5764e",
             "when": null,
@@ -2053,7 +2053,7 @@
         "genes-collection",
         "paired-collection(s)"
     ],
-    "uuid": "8f64b0be-5392-43a1-b594-d41a4dc82489",
+    "uuid": "3229a201-04e0-4818-bf3a-0a1ad8f350a2",
     "version": 1,
-    "release": "1.1"
-}
+    "release": "1.2"
+}