From 7ecd1e502c5dc09736764dd23e6b642307035a09 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 24 Feb 2025 05:41:17 +0000 Subject: [PATCH 1/2] Updating workflows/microbiome/allele-based-pathogen-identification from 0.1.2 to 0.1.3 --- .../Allele-based-Pathogen-Identification.ga | 32 +++++++++---------- .../CHANGELOG.md | 7 ++++ 2 files changed, 23 insertions(+), 16 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 2ef573362d..5c91fd3689 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": "0.1.2", + "release": "0.1.3", "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" @@ -153,7 +153,7 @@ "top": 35 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "d28b9bed-c674-406c-b58b-165bcc8eec17", @@ -243,7 +243,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -295,15 +295,15 @@ "output_name": "alignment_output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1", "tool_shed_repository": { - "changeset_revision": "5cc34c3f440d", + "changeset_revision": "66367287b4e6", "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": "2.28+galaxy0", + "tool_version": "2.28+galaxy1", "type": "tool", "uuid": "6da37636-966d-4975-bce3-d650feaeb17c", "when": null, @@ -317,7 +317,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -379,15 +379,15 @@ "output_name": "pileup" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1", "tool_shed_repository": { - "changeset_revision": "3843a30053ee", + "changeset_revision": "c9218b9dc7f0", "name": "clair3", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"qual\": \"0\", \"snp_min_af\": \"0.08\", \"indel_min_af\": \"0.15\", \"enable_phasing\": false, \"no_phasing_for_fa\": false, \"print_ref_calls\": false, \"ploidity_model\": \"--haploid_precise\", \"chunk_size\": \"5000000\"}, \"bam_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_or_vcf\": {\"bed_or_vcf_selector\": \"unrestricted\", \"__current_case__\": 2, \"include_all_ctgs\": true}, \"gvcf\": false, \"model_source\": {\"source\": \"built-in\", \"__current_case__\": 0, \"select_built_in\": \"r941_prom_hac_g360+g422\"}, \"output_files\": [\"full_alignment\", \"pileup\"], \"ref_source\": {\"source\": \"history\", \"__current_case__\": 0, \"ref_fasta\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.8+galaxy1", + "tool_state": "{\"adv\": {\"qual\": \"0\", \"snp_min_af\": \"0.08\", \"indel_min_af\": \"0.15\", \"enable_phasing\": false, \"no_phasing_for_fa\": false, \"print_ref_calls\": false, \"ploidity_model\": \"--haploid_precise\", \"chunk_size\": \"5000000\"}, \"bam_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_or_vcf\": {\"bed_or_vcf_selector\": \"unrestricted\", \"__current_case__\": 2, \"include_all_ctgs\": true}, \"gvcf\": false, \"model_source\": {\"source\": \"built-in\", \"__current_case__\": 0, \"select_built_in\": \"r941_prom_hac_g360+g422\"}, \"ont_license_agree\": false, \"output_files\": [\"full_alignment\", \"pileup\"], \"ref_source\": {\"source\": \"history\", \"__current_case__\": 0, \"ref_fasta\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.10+galaxy1", "type": "tool", "uuid": "ffbad354-41de-488d-bb37-929926bbfb31", "when": null, @@ -681,7 +681,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1", "errors": null, "id": 12, "input_connections": { @@ -709,15 +709,15 @@ "top": 617.8951200002152 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1", "tool_shed_repository": { - "changeset_revision": "3bf5661c0280", + "changeset_revision": "56a8da1f2243", "name": "table_compute", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"2\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": true}, \"user\": {\"mode\": \"matrixapply\", \"__current_case__\": 3, \"matrixapply_func\": {\"vector_op\": \"mean\", \"__current_case__\": 6}, \"dimension\": \"0\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.2.4+galaxy0", + "tool_version": "1.2.4+galaxy1", "type": "tool", "uuid": "b20b66f5-e975-4947-8935-8c628d016514", "when": null, diff --git a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md index d75f39c851..ce7bb03023 100644 --- a/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md +++ b/workflows/microbiome/allele-based-pathogen-identification/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.1.3] 2025-02-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.8+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy1` + ## [0.1.2] 2024-09-24 ### Automatic update From fd69b650160d8f9f8858417c9cd8f0c18d23dad4 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Thu, 27 Feb 2025 15:19:18 +0100 Subject: [PATCH 2/2] Fix name Really need to fix this ... --- .../Allele-based-Pathogen-Identification.ga | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 5c91fd3689..bd1491ae03 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" }, {