Mercurial > repos > greg > call_amr_mutations
view call_amr_mutations.xml @ 4:2774bdf30122 draft
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author | greg |
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date | Tue, 21 Mar 2023 19:32:25 +0000 |
parents | 30b17a17c1aa |
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<tool id="call_amr_mutations" name="PIMA: call AMR mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/call_amr_mutations.py' --varscan_raw '$varscan_raw' --output '$output' ]]></command> <inputs> <param name="varscan_raw" type="data" format="vcf" label="Raw varscan VCF file"/> </inputs> <outputs> <data name="output" format="vcf"/> </outputs> <tests> <test> <param name="varscan_raw" value="input.vcf" ftype="vcf"/> <output name="output" value="output.vcf" ftype="vcf"/> </test> </tests> <help> **What it does** Accepts VarScan mpileup2snps VCF file, filters it, and produces a filtered VCF file. </help> <expand macro="citations"/> </tool>