From c049f9c79921016064b57509e1f582436e0099ab Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 1 Apr 2024 04:31:34 +0000 Subject: [PATCH] Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.2 to 0.2.3 --- .../Scaffolding-HiC-VGP8/CHANGELOG.md | 6 + .../Scaffolding-HiC-VGP8.ga | 118 ++++++++++++++---- 2 files changed, 102 insertions(+), 22 deletions(-) diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index 63ecdebac..37ad4f7a4 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.2.3] 2024-04-01 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1` + ## [0.2.2] 2024-02-05 ### Manual update diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index 8f1783d54..fd1cd27f6 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.2.2", + "release": "0.2.3", "name": "Scaffolding-HiC-VGP8", "steps": { "0": { @@ -24,7 +24,12 @@ "errors": null, "id": 0, "input_connections": {}, - "inputs": [], + "inputs": [ + { + "description": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. \n", + "name": "Input GFA" + } + ], "label": "Input GFA", "name": "Input dataset", "outputs": [], @@ -307,7 +312,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -350,7 +360,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -399,7 +418,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -554,7 +582,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + }, + { + "description": "runtime parameter for tool YAHS", + "name": "function" + } + ], "label": null, "name": "YAHS", "outputs": [ @@ -697,7 +738,12 @@ "output_name": "final_agp_out" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -808,7 +854,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -975,7 +1026,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -1024,7 +1084,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -1073,7 +1142,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Busco", + "name": "lineage" + } + ], "label": null, "name": "Busco", "outputs": [ @@ -1130,7 +1204,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0", "tool_shed_repository": { - "changeset_revision": "2a5b8b9936bf", + "changeset_revision": "ea8146ee148f", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1246,7 +1320,7 @@ }, "2": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, "id": 2, "input_connections": { @@ -1275,15 +1349,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "fbf99087e067", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"code\": \"{total += $2; $3 = total}1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "187c2b5d-e55c-42c1-b492-0b2a7322615c", "when": null, @@ -1516,7 +1590,7 @@ } }, "tags": "", - "uuid": "c13eb98d-381a-456a-a7f7-75e880c19a17" + "uuid": "01589108-7e7f-40aa-8059-fdf5d526573c" }, "tool_id": null, "type": "subworkflow", @@ -1913,7 +1987,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "errors": null, "id": 33, "input_connections": { @@ -1944,15 +2018,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "12615d397df7", + "changeset_revision": "fbf99087e067", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"4\", \"order\": \"\", \"style\": \"\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy0", + "tool_version": "9.3+galaxy1", "type": "tool", "uuid": "88684eea-7e72-40e5-8410-d9d31a90792f", "when": null, @@ -2011,4 +2085,4 @@ ], "uuid": "a45c5bd9-6b56-40ff-a9ea-ba420a683f42", "version": 3 -} +} \ No newline at end of file