From e6b7e61167a5c1f63e36a98a5e6c343b1e68c7de Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 28 Jun 2024 09:28:32 +0000 Subject: [PATCH 1/3] Updating workflows/microbiome/allele-based-pathogen-identification from 0.1 to 0.2 --- .../Allele-based-Pathogen-Identification.ga | 34 +++++++++---------- .../CHANGELOG.md | 7 ++++ 2 files changed, 24 insertions(+), 17 deletions(-) diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index 556fe9784..c3d9656ea 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -89,7 +89,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "Bérénice Batut", + "name": "B\u00e9r\u00e9nice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -100,7 +100,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Allele-based Pathogen Identification", "report": { "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic 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), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n" @@ -243,7 +243,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", "errors": null, "id": 4, "input_connections": { @@ -295,15 +295,15 @@ "output_name": "alignment_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", "tool_shed_repository": { - "changeset_revision": "11a0d50a54e6", + "changeset_revision": "5cc34c3f440d", "name": "minimap2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"BAM\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.24+galaxy0", + "tool_version": "2.28+galaxy0", "type": "tool", "uuid": "6da37636-966d-4975-bce3-d650feaeb17c", "when": null, @@ -494,7 +494,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3", "errors": null, "id": 8, "input_connections": { @@ -534,15 +534,15 @@ "output_name": "output_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3", "tool_shed_repository": { - "changeset_revision": "da6fc9f4a367", + "changeset_revision": "ebb2e12a6de1", "name": "bcftools_norm", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"\", \"__current_case__\": 0}, \"normalize_indels\": false, \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\"}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.9+galaxy1", + "tool_state": "{\"atomize\": false, \"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"\", \"__current_case__\": 0}, \"normalize_indels\": false, \"old_rec_tag\": \"\", \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\"}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"regions_overlap\": null, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}, \"targets_overlap\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.15.1+galaxy3", "type": "tool", "uuid": "9a34ec91-725e-49b2-973b-1c508e4bdc5d", "when": null, @@ -818,7 +818,7 @@ }, "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3", "errors": null, "id": 15, "input_connections": { @@ -862,15 +862,15 @@ "output_name": "output_file" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3", "tool_shed_repository": { - "changeset_revision": "f867422772d6", + "changeset_revision": "147de996e34f", "name": "bcftools_consensus", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.9+galaxy1", + "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.15.1+galaxy3", "type": "tool", "uuid": "872ba641-1909-43ea-b3c2-62e6773583a6", "when": null, @@ -1324,4 +1324,4 @@ ], "uuid": "435875a1-72c4-4fda-8943-3a78f25c6574", "version": 72 -} +} \ No newline at end of file diff --git a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md index 90b294f63..ba38dafb8 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.2] 2024-06-28 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3` + ## [0.1] 2024-06-19 First release. From 9f6d4d52e27c96e44e8985a0ebac4b6836f3dac3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Wed, 3 Jul 2024 13:07:26 +0200 Subject: [PATCH 2/3] Update Allele-based-Pathogen-Identification.ga --- .../Allele-based-Pathogen-Identification.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index c3d9656ea..5a78e73aa 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -89,7 +89,7 @@ { "class": "Person", "identifier": "0000-0001-9852-1987", - "name": "B\u00e9r\u00e9nice Batut", + "name": "Bérénice Batut", "url": "https://orcid.org/0000-0001-9852-1987" }, { @@ -1324,4 +1324,4 @@ ], "uuid": "435875a1-72c4-4fda-8943-3a78f25c6574", "version": 72 -} \ No newline at end of file +} From 865ab7797d658f30251f6bd4a87853ce51359127 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 3 Jul 2024 13:40:11 +0200 Subject: [PATCH 3/3] Make automated update a patch bump --- .../Allele-based-Pathogen-Identification.ga | 2 +- .../allele-based-pathogen-identification/CHANGELOG.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga index 5a78e73aa..a41070e3f 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga +++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification.ga @@ -100,7 +100,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2", + "release": "0.1.1", "name": "Allele-based Pathogen Identification", "report": { "markdown": "# Allele-based Pathogen Identification Workflow Report\nBelow are the results for the Allele based Pathogenic 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), and a FASTA file of the reference genome of the main Pathogen identified in the Gene based Pathogen Identification workflow, or per-known to the user.\n\n## Workflow Output: \n\n### All variants found per sample against the reference genome\n\n```galaxy\nhistory_dataset_display(output=\"extracted_fields_from_the_vcf_output\")\n```\n\n### Number of variants per sample\n\n```galaxy\nhistory_dataset_display(output=\"number_of_variants_per_sample\")\n```\n\n### Mapping mean depth of coverage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_mean_depth_per_sample\")\n```\n\n### Mapping breadth of coverage percentage per sample\n\n```galaxy\nhistory_dataset_display(output=\"mapping_coverage_percentage_per_sample\")\n```\n\n" diff --git a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md index ba38dafb8..e13bf3593 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/allele-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/iuc/minimap2/minimap2/2.24+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0`