Mercurial > repos > iuc > cnv_vcf2json
diff cnv-vcf2json.xml @ 0:c8caf812d33b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 485fd56c701872217e6d6ccc4321c1f0522ad540
author | iuc |
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date | Fri, 01 Mar 2024 07:19:35 +0000 |
parents | |
children | 7d2d2e3b9891 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cnv-vcf2json.xml Fri Mar 01 07:19:35 2024 +0000 @@ -0,0 +1,31 @@ +<tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Converts 1000hg structural variants VCF file to JSON</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="creators"/> + <command detect_errors="exit_code"><![CDATA[ + #import re + ln -s '$input_vcf_file' ./input.vcf && + cnv-vcf2json + -i ./input.vcf + -o output.json + ]]></command> + <inputs> + <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" /> + </inputs> + <outputs> + <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" /> + <output name="output_json" file="output.json" /> + </test> + </tests> + <help><![CDATA[ + The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol + ]]></help> + <expand macro="citations"/> +</tool>