From 697f7864c315debb3a2c6e4846a65f5247cb5bf9 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 4 Mar 2024 04:58:41 +0000 Subject: [PATCH] Updating workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7 from 0.1.1 to 0.1.2 --- .../Scaffolding-Bionano-VGP7/CHANGELOG.md | 5 + .../Scaffolding-BioNano-VGP7.ga | 138 +++++++++++++++--- 2 files changed, 122 insertions(+), 21 deletions(-) diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md index 3ce415e35..7c8537fc6 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.2] 2024-03-04 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` + ## [0.1.1] 2023-11-14 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga index dfad81092..051322a18 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga @@ -14,7 +14,7 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.1", + "release": "0.1.2", "name": "Scaffolding-BioNano-VGP7", "steps": { "0": { @@ -142,7 +142,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -182,6 +187,10 @@ } }, "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, { "description": "runtime parameter for tool gfastats", "name": "mode_condition" @@ -233,7 +242,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Bionano Hybrid Scaffold", + "name": "bionano_cmap" + }, + { + "description": "runtime parameter for tool Bionano Hybrid Scaffold", + "name": "conflict_resolution" + }, + { + "description": "runtime parameter for tool Bionano Hybrid Scaffold", + "name": "ngs_fasta" + } + ], "label": null, "name": "Bionano Hybrid Scaffold", "outputs": [ @@ -352,7 +374,16 @@ "output_name": "ngs_contigs_scaffold_agp" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, + { + "description": "runtime parameter for tool gfastats", + "name": "mode_condition" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -413,6 +444,10 @@ } }, "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + }, { "description": "runtime parameter for tool gfastats", "name": "mode_condition" @@ -474,7 +509,12 @@ "output_name": "integer_param" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -527,7 +567,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool gfastats", + "name": "input_file" + } + ], "label": null, "name": "gfastats", "outputs": [ @@ -576,6 +621,7 @@ "subworkflow": { "a_galaxy_workflow": "true", "annotation": "", + "comments": [], "format-version": "0.1", "name": "gfastats_data_prep", "steps": { @@ -617,7 +663,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "input" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -647,7 +698,7 @@ }, "2": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "errors": null, "id": 2, "input_connections": { @@ -656,7 +707,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Text reformatting", + "name": "infile" + } + ], "label": null, "name": "Text reformatting", "outputs": [ @@ -676,15 +732,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "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": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "69c7b2e7-5c82-49ec-8301-737e5ec1739b", "when": null, @@ -701,7 +757,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -746,7 +807,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Add column", + "name": "input" + } + ], "label": null, "name": "Add column", "outputs": [ @@ -785,7 +851,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Parse parameter value", + "name": "input1" + } + ], "label": null, "name": "Parse parameter value", "outputs": [ @@ -873,7 +944,12 @@ "output_name": "out1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -917,7 +993,7 @@ } }, "tags": "", - "uuid": "ee2567e9-9666-43d3-9bf9-939b48e56573" + "uuid": "8c62f0a6-3009-43d0-b986-5a7909c91474" }, "tool_id": null, "type": "subworkflow", @@ -936,7 +1012,12 @@ "output_name": "gfastats data for plotting" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -975,7 +1056,12 @@ "output_name": "gfastats data for plotting" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1014,7 +1100,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": null, "name": "Scatterplot with ggplot2", "outputs": [ @@ -1067,7 +1158,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Scatterplot with ggplot2", + "name": "input1" + } + ], "label": null, "name": "Scatterplot with ggplot2", "outputs": [