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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 1a82c0609363fe0541e6dbdd46308a67f30ca9e1-dirty
author | jjohnson |
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date | Mon, 20 May 2019 15:30:06 -0400 |
parents | 63f23d5db27c |
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<?xml version="1.0"?> <tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="@DEFUSE_VERSION@.2"> <description>generate a VCF from a DeFuse Results file</description> <macros> <import>macros.xml</import> </macros> <command detect_errors="default"><![CDATA[ $__tool_directory__/defuse_results_to_vcf.py --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf ]]></command> <inputs> <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> </inputs> <outputs> <data name="vcf" metadata_source="defuse_results" format="vcf"/> </outputs> <tests> <test> <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/> <output name="vcf" file="mm10_results.filtered.vcf"/> </test> </tests> <help> **Defuse Results to VCF** Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file. This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file. .. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse </help> </tool>