Mercurial > repos > iuc > cnv_vcf2json
changeset 1:7d2d2e3b9891 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
| author | iuc |
|---|---|
| date | Wed, 24 Jul 2024 12:56:03 +0000 |
| parents | c8caf812d33b |
| children | |
| files | cnv-vcf2json.xml macros.xml test-data/output.json |
| diffstat | 3 files changed, 7868 insertions(+), 3729 deletions(-) [+] |
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--- a/cnv-vcf2json.xml Fri Mar 01 07:19:35 2024 +0000 +++ b/cnv-vcf2json.xml Wed Jul 24 12:56:03 2024 +0000 @@ -21,7 +21,9 @@ <tests> <test expect_num_outputs="1"> <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" /> - <output name="output_json" file="output.json" /> + <output name="output_json" file="output.json" ftype="json" compare="sim_size" > + <assert_contents><has_size value="356000" delta="20000" /></assert_contents> + </output> </test> </tests> <help><![CDATA[
--- a/macros.xml Fri Mar 01 07:19:35 2024 +0000 +++ b/macros.xml Wed Jul 24 12:56:03 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">1.0.4</token> + <token name="@VERSION_SUFFIX@">0.1</token> + <token name="@TOOL_VERSION@">1.1.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">cnv-vcf2json</requirement>
--- a/test-data/output.json Fri Mar 01 07:19:35 2024 +0000 +++ b/test-data/output.json Wed Jul 24 12:56:03 2024 +0000 @@ -3,8865 +3,13002 @@ "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:2650427-2651463:EFO:0030069", - "variantType": "DEL", - "variantId": "EFO:0030069", - "start": 2650427, - "end": 2651463, - "referenceName": "1", + "variantState": { + "id": "EFO:0030069", + "label": "complete genomic loss" + }, + "definitions": { + "Location": { + "start": 2650427, + "end": 2651463, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463", "cnCount": 0, "cnValue": 1.00369e-09 - } + }, + "updated": "2024-07-24T09:24:38.692461" }, { "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:2651463-2653075:EFO:0030068", - "variantType": "DEL", - "variantId": "EFO:0030068", - "start": 2651463, - "end": 2653075, - "referenceName": "1", + "variantState": { + "id": "EFO:0030068", + "label": "low-level loss" + }, + "definitions": { + "Location": { + "start": 2651463, + "end": 2653075, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075", "cnCount": 1, "cnValue": 0.395524 - } + }, + "updated": "2024-07-24T09:24:38.692482" }, { "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:4063594-4067475:EFO:0030068", - "variantType": "DEL", - "variantId": "EFO:0030068", - "start": 4063594, - "end": 4067475, - "referenceName": "1", + "variantState": { + "id": "EFO:0030068", + "label": "low-level loss" + }, + "definitions": { + "Location": { + "start": 4063594, + "end": 4067475, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:LOSS:chr1:4063595-4067475", "cnCount": 1, "cnValue": 0.429788 - } + }, + "updated": "2024-07-24T09:24:38.692495" }, { "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:6377770-6385660:EFO:0030068", - "variantType": "DEL", - "variantId": "EFO:0030068", - "start": 6377770, - "end": 6385660, - "referenceName": "1", + "variantState": { + "id": "EFO:0030068", + "label": "low-level loss" + }, + "definitions": { + "Location": { + "start": 6377770, + "end": 6385660, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:LOSS:chr1:6377771-6385660", "cnCount": 1, "cnValue": 0.543097 - } + }, + "updated": "2024-07-24T09:24:38.692503" }, { "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:8143311-8150440:EFO:0030071", - "variantType": "DUP", - "variantId": "EFO:0030071", - "start": 8143311, - "end": 8150440, - "referenceName": "1", + "variantState": { + "id": "EFO:0030071", + "label": "low-level gain" + }, + "definitions": { + "Location": { + "start": 8143311, + "end": 8150440, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:GAIN:chr1:8143312-8150440", "cnCount": 3, "cnValue": 1.42495 - } + }, + "updated": "2024-07-24T09:24:38.692512" }, { "biosampleId": "HG00096", "assemblyId": "GRCh38", "variantInternalId": "chr1:13224579-13242034:EFO:0030071", - "variantType": "DUP", - "variantId": "EFO:0030071", - "start": 13224579, - "end": 13242034, - "referenceName": "1", + "variantState": { + "id": "EFO:0030071", + "label": "low-level gain" + }, + "definitions": { + "Location": { + "start": 13224579, + "end": 13242034, + "chromosome": "1" + } + }, "info": { "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034", "cnCount": 3, "cnValue": 1.49181 - 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