From 6c30ccbbcb302e2da5cc989bb9c60806ea5c5e01 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 30 Sep 2024 14:41:28 +0000 Subject: [PATCH 1/3] Updating workflows/bacterial_genomics/amr_gene_detection from 1.1.2 to 1.1.3 --- .../amr_gene_detection/CHANGELOG.md | 6 ++++++ .../amr_gene_detection/amr_gene_detection.ga | 18 +++++++++--------- 2 files changed, 15 insertions(+), 9 deletions(-) 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.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, From dad1a0e7c8e310e40f7cbf7391ceb098738db1f6 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 30 Sep 2024 14:42:58 +0000 Subject: [PATCH 2/3] Updating workflows/bacterial_genomics/bacterial_genome_annotation from 1.1.4 to 1.1.5 --- .../bacterial_genome_annotation/CHANGELOG.md | 6 ++++++ .../bacterial_genome_annotation.ga | 18 +++++++++--------- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md index 53693c435..a484bdfad 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [1.1.5] 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` + ## [1.1.4] 2024-09-19 ### Manual 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 index e1bbf657e..17b5af4c6 100644 --- 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": "1.1.4", + "release": "1.1.5", "name": "bacterial_genome_annotation", "steps": { "0": { @@ -982,7 +982,7 @@ }, "8": { "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": 8, "input_connections": { @@ -1120,15 +1120,15 @@ "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\": \"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", + "tool_version": "0.9.1+galaxy0", "type": "tool", "uuid": "678bdbfe-7a3a-4a91-8ea7-1cb17f53daa6", "when": null, @@ -1142,7 +1142,7 @@ }, "9": { "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": 9, "input_connections": { @@ -1180,15 +1180,15 @@ "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": "3427b1f1-79ce-4ade-a350-baf15ac250c2", "when": null, From 4cf41e91f7bd370484fd9c889c79627e0738cdd4 Mon Sep 17 00:00:00 2001 From: Clea Siguret Date: Wed, 2 Oct 2024 15:25:45 +0200 Subject: [PATCH 3/3] Fix test --- .../amr_gene_detection/amr_gene_detection-tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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"