# HG changeset patch
# User iuc
# Date 1721825763 0
# Node ID 7d2d2e3b9891ada9931a874a0e1d27b01a758f34
# Parent c8caf812d33be5afa27593c86d041494443c7c1f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
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
@@ -21,7 +21,9 @@
-
+
- 0
- 1.0.4
+ 0.1
+ 1.1.0
cnv-vcf2json
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
@@ -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
- }
- },
- {
- "biosampleId": "HG00096",
- "assemblyId": "GRCh38",
- "variantInternalId": "chr1:16605061-16646293:EFO:0030071",
- "variantType": "DUP",
- "variantId": "EFO:0030071",
- "start": 16605061,
- "end": 16646293,
- "referenceName": "1",
+ },
+ "updated": "2024-07-24T09:24:38.692520"
+ },
+ {
+ "biosampleId": "HG00096",
+ "assemblyId": "GRCh38",
+ "variantInternalId": "chr1:16605061-16646293:EFO:0030072",
+ "variantState": {
+ "id": "EFO:0030072",
+ "label": "high-level gain"
+ },
+ "definitions": {
+ "Location": {
+ "start": 16605061,
+ "end": 16646293,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:GAIN:chr1:16605062-16646293",
"cnCount": 7,
"cnValue": 3.3289
- }
- },
- {
- "biosampleId": "HG00096",
- "assemblyId": "GRCh38",
- "variantInternalId": "chr1:16716711-16728256:EFO:0030071",
- "variantType": "DUP",
- "variantId": "EFO:0030071",
- "start": 16716711,
- "end": 16728256,
- "referenceName": "1",
+ },
+ "updated": "2024-07-24T09:24:38.692529"
+ },
+ {
+ "biosampleId": "HG00096",
+ "assemblyId": "GRCh38",
+ "variantInternalId": "chr1:16716711-16728256:EFO:0030072",
+ "variantState": {
+ "id": "EFO:0030072",
+ "label": "high-level gain"
+ },
+ "definitions": {
+ "Location": {
+ "start": 16716711,
+ "end": 16728256,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:GAIN:chr1:16716712-16728256",
"cnCount": 5,
"cnValue": 2.68822
- }
+ },
+ "updated": "2024-07-24T09:24:38.692539"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:16879751-16950196:EFO:0030071",
- "variantType": "DUP",
- "variantId": "EFO:0030071",
- "start": 16879751,
- "end": 16950196,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030071",
+ "label": "low-level gain"
+ },
+ "definitions": {
+ "Location": {
+ "start": 16879751,
+ "end": 16950196,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:GAIN:chr1:16879752-16950196",
"cnCount": 3,
"cnValue": 1.53152
- }
+ },
+ "updated": "2024-07-24T09:24:38.692546"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:34636777-34646300:EFO:0030068",
- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 34636777,
- "end": 34646300,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
+ "Location": {
+ "start": 34636777,
+ "end": 34646300,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:34636778-34646300",
"cnCount": 1,
"cnValue": 0.495288
- }
+ },
+ "updated": "2024-07-24T09:24:38.692554"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:36957723-36960386:EFO:0030068",
- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 36957723,
- "end": 36960386,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
+ "Location": {
+ "start": 36957723,
+ "end": 36960386,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:36957724-36960386",
"cnCount": 1,
"cnValue": 0.479029
- }
+ },
+ "updated": "2024-07-24T09:24:38.692561"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:43593157-43594353:EFO:0030068",
- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 43593157,
- "end": 43594353,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
+ "Location": {
+ "start": 43593157,
+ "end": 43594353,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:43593158-43594353",
"cnCount": 1,
"cnValue": 0.289679
- }
+ },
+ "updated": "2024-07-24T09:24:38.692568"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:58278107-58279217:EFO:0030069",
- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 58278107,
- "end": 58279217,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030069",
+ "label": "complete genomic loss"
+ },
+ "definitions": {
+ "Location": {
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+ "end": 58279217,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:58278108-58279217",
"cnCount": 0,
"cnValue": 0.0937719
- }
+ },
+ "updated": "2024-07-24T09:24:38.692575"
},
{
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"assemblyId": "GRCh38",
"variantInternalId": "chr1:61647700-61655464:EFO:0030068",
- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 61647700,
- "end": 61655464,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
+ "Location": {
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+ "end": 61655464,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:61647701-61655464",
"cnCount": 1,
"cnValue": 0.52381
- }
+ },
+ "updated": "2024-07-24T09:24:38.692589"
},
{
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- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 62188614,
- "end": 62191346,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
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+ "end": 62191346,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:62188615-62191346",
"cnCount": 1,
"cnValue": 0.483858
- }
+ },
+ "updated": "2024-07-24T09:24:38.692597"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 67542030,
- "end": 67543275,
- "referenceName": "1",
+ "variantState": {
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+ "label": "complete genomic loss"
+ },
+ "definitions": {
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+ "end": 67543275,
+ "chromosome": "1"
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"info": {
"legacyId": "DRAGEN:LOSS:chr1:67542031-67543275",
"cnCount": 0,
"cnValue": 0.0312573
- }
+ },
+ "updated": "2024-07-24T09:24:38.692603"
},
{
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"assemblyId": "GRCh38",
"variantInternalId": "chr1:72289205-72345923:EFO:0030068",
- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 72289205,
- "end": 72345923,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
+ "Location": {
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+ "end": 72345923,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:72289206-72345923",
"cnCount": 1,
"cnValue": 0.486641
- }
+ },
+ "updated": "2024-07-24T09:24:38.692610"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 78183859,
- "end": 78192785,
- "referenceName": "1",
+ "variantState": {
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+ "label": "low-level loss"
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+ "definitions": {
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+ "end": 78192785,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:78183860-78192785",
"cnCount": 1,
"cnValue": 0.482922
- }
+ },
+ "updated": "2024-07-24T09:24:38.692617"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 89010497,
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- "referenceName": "1",
+ "variantState": {
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+ "label": "complete genomic loss"
+ },
+ "definitions": {
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+ "end": 89012783,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:89010498-89012783",
"cnCount": 0,
"cnValue": 1.00369e-09
- }
+ },
+ "updated": "2024-07-24T09:24:38.692624"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 103362730,
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- "referenceName": "1",
+ "variantState": {
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+ "label": "low-level loss"
+ },
+ "definitions": {
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+ "end": 103365638,
+ "chromosome": "1"
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+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:103362731-103365638",
"cnCount": 1,
"cnValue": 0.320331
- }
+ },
+ "updated": "2024-07-24T09:24:38.692634"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 105472899,
- "end": 105480377,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
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+ "end": 105480377,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:105472900-105480377",
"cnCount": 1,
"cnValue": 0.450727
- }
+ },
+ "updated": "2024-07-24T09:24:38.692641"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 109644578,
- "end": 109647981,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030069",
+ "label": "complete genomic loss"
+ },
+ "definitions": {
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+ "end": 109647981,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:109644579-109647981",
"cnCount": 0,
"cnValue": 1.00369e-09
- }
+ },
+ "updated": "2024-07-24T09:24:38.692650"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030068",
- "start": 109647981,
- "end": 109650349,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030068",
+ "label": "low-level loss"
+ },
+ "definitions": {
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+ "end": 109650349,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:109647982-109650349",
"cnCount": 1,
"cnValue": 0.587163
- }
+ },
+ "updated": "2024-07-24T09:24:38.692657"
},
{
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"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 109687569,
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- "referenceName": "1",
+ "variantState": {
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+ "label": "complete genomic loss"
+ },
+ "definitions": {
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+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:109687570-109697444",
"cnCount": 0,
"cnValue": 1.00369e-09
- }
+ },
+ "updated": "2024-07-24T09:24:38.692664"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
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- "variantType": "DEL",
- "variantId": "EFO:0030069",
- "start": 112148880,
- "end": 112161897,
- "referenceName": "1",
+ "variantState": {
+ "id": "EFO:0030069",
+ "label": "complete genomic loss"
+ },
+ "definitions": {
+ "Location": {
+ "start": 112148880,
+ "end": 112161897,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:LOSS:chr1:112148881-112161897",
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"cnValue": 1.00369e-09
- }
- },
- {
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- "variantType": "DUP",
- "variantId": "EFO:0030071",
- "start": 125073511,
- "end": 125084673,
- "referenceName": "1",
+ },
+ "updated": "2024-07-24T09:24:38.692671"
+ },
+ {
+ "biosampleId": "HG00096",
+ "assemblyId": "GRCh38",
+ "variantInternalId": "chr1:125073511-125084673:EFO:0030072",
+ "variantState": {
+ "id": "EFO:0030072",
+ "label": "high-level gain"
+ },
+ "definitions": {
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+ "end": 125084673,
+ "chromosome": "1"
+ }
+ },
"info": {
"legacyId": "DRAGEN:GAIN:chr1:125073512-125084673",
"cnCount": 5,
"cnValue": 2.35809
- }
+ },
+ "updated": "2024-07-24T09:24:38.692684"
},
{
"biosampleId": "HG00096",
"assemblyId": "GRCh38",
"variantInternalId": "chr1:125084673-125170990:EFO:0030071",
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]
\ No newline at end of file