Repository 'cnv_vcf2json'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/cnv_vcf2json

Changeset 1:7d2d2e3b9891 (2024-07-24)
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
b
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 @@
     <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
b
@@ -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
b
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'