diff --git a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md index 0ae8f3667..bbeba9871 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md +++ b/workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.1.3] 2024-09-30 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` + ## [1.1.2] 2024-09-19 ### Manual update diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml index 254a6b403..a3ef9036f 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml @@ -54,9 +54,9 @@ n: 15 tooldistillator_summarize: asserts: - has_text: + - that: "has_text" text: "% Identity to reference sequence" - has_text: + - that: "has_text" text: "Enterococcus faecalis V583" - has_text: - text: "CGE Predicted Phenotype" + - that: "has_text" + text: "Fibrinogen binding protein" diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga index a11f7e612..9f83b43bc 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga @@ -27,7 +27,7 @@ ], "format-version": "0.1", "license": "GPL-3.0-or-later", - "release": "1.1.2", + "release": "1.1.3", "name": "amr_gene_detection", "steps": { "0": { @@ -528,7 +528,7 @@ }, "7": { "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/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -598,15 +598,15 @@ "output_name": "output_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "a7387ce2a8ca", + "changeset_revision": "8d6686664021", "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\"}, \"analysis_software_version\": \"1.0.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"staramr\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mlst_file_path\": {\"__class__\": \"ConnectedValue\"}, \"plasmidfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"pointfinder_file_path\": {\"__class__\": \"RuntimeValue\"}, \"setting_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.10.0\", \"reference_database_version\": null}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"amrfinderplus\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"point_mutation_report_path\": {\"__class__\": \"ConnectedValue\"}, \"nucleotide_sequence_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.12.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "1589f8a1-65b6-43f0-9e75-cad9b1752e5c", "when": null, @@ -620,7 +620,7 @@ }, "8": { "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/0.9+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "errors": null, "id": 8, "input_connections": { @@ -658,15 +658,15 @@ "output_name": "summary_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "def7a82d23e1", + "changeset_revision": "f3233d395549", "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": "0.9+galaxy0", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "a88f6b82-502c-46cf-a174-2c8361e8e8dd", "when": null,