From 589bd96d268294cd4a614fadbf82f8ac7bfecb51 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 28 Jun 2024 09:30:32 +0000 Subject: [PATCH 1/3] Updating workflows/microbiome/gene-based-pathogen-identification from 0.1 to 0.2 --- .../CHANGELOG.md | 8 +++ .../Gene-based-Pathogen-Identification.ga | 58 +++++++++---------- 2 files changed, 37 insertions(+), 29 deletions(-) diff --git a/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md index e86703065..4116304fa 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [0.2] 2024-06-28 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2` +- `toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1` + ## [0.1] 2024-04-18 First release. diff --git a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga index 8be13a1c8..65a2654f7 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga +++ b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga @@ -100,7 +100,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "Bérénice Batut", + "name": "B\u00e9r\u00e9nice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -111,7 +111,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Gene-based Pathogen Identification", "report": { "markdown": "# Gene-based Pathogen Identification Workflow Report\n\nBelow are the results for the Gene based Pathogen Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Output\n\n### Identified contigs per sample\n\n```galaxy\nhistory_dataset_display(output=\"contigs\")\n```\n\n### Identified pathogenic genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"vfs\")\n```\n\n### Identified Antimicrobial Resistance genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"amrs\")\n```\n" @@ -246,7 +246,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "errors": null, "id": 3, "input_connections": { @@ -282,15 +282,15 @@ "output_name": "list_output_txt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2", "tool_shed_repository": { - "changeset_revision": "6cbe2f30c2d7", + "changeset_revision": "2dae863c8f42", "name": "split_file_to_collection", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"split_parms\": {\"select_ftype\": \"txt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"split_file\", \"select_allocate\": {\"allocate\": \"byrow\", \"__current_case__\": 2}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.5.0", + "tool_version": "0.5.2", "type": "tool", "uuid": "f1e00cb8-a264-4acb-aff6-8c8b5aa0b48b", "when": null, @@ -304,7 +304,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -368,15 +368,15 @@ "output_name": "consensus" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "cb8dfd28c16f", + "changeset_revision": "291923e6f276", "name": "flye", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": false, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"meta\": true, \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--nano-hq\", \"__current_case__\": 2}, \"no_alt_contigs\": false, \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.9.1+galaxy0", + "tool_version": "2.9.3+galaxy0", "type": "tool", "uuid": "a343c482-44b1-4cb3-a46e-2e714f785960", "when": null, @@ -452,7 +452,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -531,15 +531,15 @@ "output_name": "out_probs" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "79e9a869f40e", + "changeset_revision": "fc8804320156", "name": "medaka_consensus_pipeline", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_hac_g507\", \"out\": [\"consensus\", \"probs\", \"calls\", \"log\", \"gaps\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.7.2+galaxy0", + "tool_version": "1.7.2+galaxy1", "type": "tool", "uuid": "9e88fc55-f41e-4e87-852e-044359dcea53", "when": null, @@ -765,7 +765,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1", "tool_shed_repository": { - "changeset_revision": "3f3e247c053d", + "changeset_revision": "c2ef298da409", "name": "abricate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -825,7 +825,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1", "tool_shed_repository": { - "changeset_revision": "3f3e247c053d", + "changeset_revision": "c2ef298da409", "name": "abricate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -845,7 +845,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 12, "input_connections": { @@ -880,15 +880,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "fbf99087e067", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"column\", \"__current_case__\": 1, \"column\": \"1\"}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "4de0cdf1-967a-4c47-9c95-f1f129ad5810", "when": null, @@ -902,7 +902,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 13, "input_connections": { @@ -944,15 +944,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "fbf99087e067", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#FILE\", \"replace_pattern\": \"SampleID\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"column\", \"__current_case__\": 1, \"column\": \"1\"}}, {\"__index__\": 1, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": true, \"searchwhere\": {\"searchwhere_select\": \"column\", \"__current_case__\": 1, \"column\": \"2\"}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "4e5b87e2-4743-44d3-b57d-b5cab2887e46", "when": null, @@ -966,7 +966,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "errors": null, "id": 14, "input_connections": { @@ -1008,15 +1008,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "fbf99087e067", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"#FILE\", \"replace_pattern\": \"SampleID\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"column\", \"__current_case__\": 1, \"column\": \"1\"}}, {\"__index__\": 1, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": true, \"searchwhere\": {\"searchwhere_select\": \"column\", \"__current_case__\": 1, \"column\": \"2\"}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "9ebff4c8-3b3c-43a1-a008-490b4745f407", "when": null, @@ -1097,4 +1097,4 @@ ], "uuid": "d6795753-1562-4ccc-8f9c-f598acd5404e", "version": 142 -} +} \ No newline at end of file From cdd8660e740967c811f9955f96de49e37d879f94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 3 Jul 2024 13:06:41 +0200 Subject: [PATCH 2/3] Update Gene-based-Pathogen-Identification.ga --- .../Gene-based-Pathogen-Identification.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga index 65a2654f7..98657d695 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga +++ b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga @@ -100,7 +100,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -1097,4 +1097,4 @@ ], "uuid": "d6795753-1562-4ccc-8f9c-f598acd5404e", "version": 142 -} \ No newline at end of file +} From 66f0c312a3bc28bdbeb9f2a33f6cae520107a6ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 10 Jul 2024 10:05:55 +0200 Subject: [PATCH 3/3] Apply suggestions from code review --- .../microbiome/gene-based-pathogen-identification/CHANGELOG.md | 2 +- .../Gene-based-Pathogen-Identification.ga | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md index 4116304fa..355c4b16e 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/gene-based-pathogen-identification/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## [0.2] 2024-06-28 +## [0.1.1] 2024-06-28 ### Automatic update - `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2` diff --git a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga index 98657d695..ab5c55e5d 100644 --- a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga +++ b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification.ga @@ -111,7 +111,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2", + "release": "0.1.1", "name": "Gene-based Pathogen Identification", "report": { "markdown": "# Gene-based Pathogen Identification Workflow Report\n\nBelow are the results for the Gene based Pathogen Identification Workflow\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Workflow Inputs\nThe Perprocessing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Output\n\n### Identified contigs per sample\n\n```galaxy\nhistory_dataset_display(output=\"contigs\")\n```\n\n### Identified pathogenic genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"vfs\")\n```\n\n### Identified Antimicrobial Resistance genes per sample\n\n```galaxy\nhistory_dataset_display(output=\"amrs\")\n```\n"