Mercurial > repos > iuc > cnv_vcf2json
comparison cnv-vcf2json.xml @ 0:9be5490bb681 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
| author | iuc |
|---|---|
| date | Wed, 24 Jul 2024 12:53:58 +0000 |
| parents | |
| children | 6763389420f5 |
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| -1:000000000000 | 0:9be5490bb681 |
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| 1 <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Converts 1000hg structural variants VCF file to JSON</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <expand macro="creators"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 #import re | |
| 10 ln -s '$input_vcf_file' ./input.vcf && | |
| 11 cnv-vcf2json | |
| 12 -i ./input.vcf | |
| 13 -o output.json | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" /> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test expect_num_outputs="1"> | |
| 23 <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" /> | |
| 24 <output name="output_json" file="output.json" ftype="json" compare="sim_size" > | |
| 25 <assert_contents><has_size value="356000" delta="20000" /></assert_contents> | |
| 26 </output> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol | |
| 31 ]]></help> | |
| 32 <expand macro="citations"/> | |
| 33 </tool> |