Previous changeset 0:c8caf812d33b (2024-03-01) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d |
modified:
cnv-vcf2json.xml macros.xml test-data/output.json |
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diff -r c8caf812d33b -r 7d2d2e3b9891 cnv-vcf2json.xml --- a/cnv-vcf2json.xml Fri Mar 01 07:19:35 2024 +0000 +++ b/cnv-vcf2json.xml Wed Jul 24 12:56:03 2024 +0000 |
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@@ -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[ |
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diff -r c8caf812d33b -r 7d2d2e3b9891 macros.xml --- a/macros.xml Fri Mar 01 07:19:35 2024 +0000 +++ b/macros.xml Wed Jul 24 12:56:03 2024 +0000 |
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@@ -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> |
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diff -r c8caf812d33b -r 7d2d2e3b9891 test-data/output.json --- 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 |
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b'@@ -3,8865 +3,13002 @@\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chr1:2650427-2651463:EFO:0030069",\n- "variantType": "DEL",\n- "variantId": "EFO:0030069",\n- "start": 2650427,\n- "end": 2651463,\n- "referenceName": "1",\n+ "variantState": {\n+ "id": "EFO:0030069",\n+ "label": "complete genomic loss"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 2650427,\n+ "end": 2651463,\n+ "chromosome": "1"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463",\n "cnCount": 0,\n "cnValue": 1.00369e-09\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.692461"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chr1:2651463-2653075:EFO:0030068",\n- "variantType": "DEL",\n- "variantId": "EFO:0030068",\n- "start": 2651463,\n- "end": 2653075,\n- "referenceName": "1",\n+ "variantState": {\n+ "id": "EFO:0030068",\n+ "label": "low-level loss"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 2651463,\n+ "end": 2653075,\n+ "chromosome": "1"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075",\n "cnCount": 1,\n "cnValue": 0.395524\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.692482"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chr1:4063594-4067475:EFO:0030068",\n- "variantType": "DEL",\n- "variantId": "EFO:0030068",\n- "start": 4063594,\n- "end": 4067475,\n- "referenceName": "1",\n+ "variantState": {\n+ "id": "EFO:0030068",\n+ "label": "low-level loss"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 4063594,\n+ "end": 4067475,\n+ "chromosome": "1"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:LOSS:chr1:4063595-4067475",\n "cnCount": 1,\n "cnValue": 0.429788\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.692495"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chr1:6377770-6385660:EFO:0030068",\n- "variantType": "DEL",\n- "variantId": "EFO:0030068",\n- "start": 6377770,\n- "end": 6385660,\n- "referenceName": "1",\n+ "variantState": {\n+ "id": "EFO:0030068",\n+ "label": "low-level loss"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 6377770,\n+ "end": 6385660,\n+ "chromosome": "1"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:LOSS:chr1:6377771-6385660",\n "cnCount": 1,\n "cnValue": 0.543097\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.692503"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chr1:8143311-8150440:EFO:0030071",\n- "variantType": "DUP",\n- "variantId": "EFO:0030071",\n- "start": 8143311,\n- "end": 8150440,\n- "referenceName": "1",\n+ "variantState": {\n+ "id": "EFO:0030071",\n+ "label": "low-level gain"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 8143311,\n+ "end": 8150440,\n+ "chromosome": "1"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:GAIN:chr1:8143312-8150440",\n "cnCount": 3,\n "cnValue": 1.42495\n- }\n+ '..b'9947-11296309:EFO:0030072",\n+ "variantState": {\n+ "id": "EFO:0030072",\n+ "label": "high-level gain"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 11289947,\n+ "end": 11296309,\n+ "chromosome": "Y"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:GAIN:chrY:11289948-11296309",\n "cnCount": 26,\n "cnValue": 26.0609\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.697933"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chrY:11296309-11330116:EFO:0030070",\n- "variantType": "DUP",\n- "variantId": "EFO:0030070",\n- "start": 11296309,\n- "end": 11330116,\n- "referenceName": "Y",\n+ "variantState": {\n+ "id": "EFO:0030070",\n+ "label": "copy number gain"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 11296309,\n+ "end": 11330116,\n+ "chromosome": "Y"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:GAIN:chrY:11296310-11330116",\n "cnCount": 2,\n "cnValue": 1.84192\n- }\n- },\n- {\n- "biosampleId": "HG00096",\n- "assemblyId": "GRCh38",\n- "variantInternalId": "chrY:11530585-11539539:EFO:0030071",\n- "variantType": "DUP",\n- "variantId": "EFO:0030071",\n- "start": 11530585,\n- "end": 11539539,\n- "referenceName": "Y",\n+ },\n+ "updated": "2024-07-24T09:24:38.697940"\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11530585-11539539:EFO:0030072",\n+ "variantState": {\n+ "id": "EFO:0030072",\n+ "label": "high-level gain"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 11530585,\n+ "end": 11539539,\n+ "chromosome": "Y"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:GAIN:chrY:11530586-11539539",\n "cnCount": 17,\n "cnValue": 16.6986\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.697947"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chrY:11744914-11748800:EFO:0030070",\n- "variantType": "DUP",\n- "variantId": "EFO:0030070",\n- "start": 11744914,\n- "end": 11748800,\n- "referenceName": "Y",\n+ "variantState": {\n+ "id": "EFO:0030070",\n+ "label": "copy number gain"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 11744914,\n+ "end": 11748800,\n+ "chromosome": "Y"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:GAIN:chrY:11744915-11748800",\n "cnCount": 2,\n "cnValue": 2.03175\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.697954"\n },\n {\n "biosampleId": "HG00096",\n "assemblyId": "GRCh38",\n "variantInternalId": "chrY:12512335-12514483:EFO:0030069",\n- "variantType": "DEL",\n- "variantId": "EFO:0030069",\n- "start": 12512335,\n- "end": 12514483,\n- "referenceName": "Y",\n+ "variantState": {\n+ "id": "EFO:0030069",\n+ "label": "complete genomic loss"\n+ },\n+ "definitions": {\n+ "Location": {\n+ "start": 12512335,\n+ "end": 12514483,\n+ "chromosome": "Y"\n+ }\n+ },\n "info": {\n "legacyId": "DRAGEN:LOSS:chrY:12512336-12514483",\n "cnCount": 0,\n "cnValue": 0.284822\n- }\n+ },\n+ "updated": "2024-07-24T09:24:38.697961"\n }\n ]\n\\ No newline at end of file\n' |