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author | greg |
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date | Wed, 19 Dec 2018 08:58:27 -0500 |
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<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@"> <description>sort VCF/BCF files</description> <macros> <token name="@EXECUTABLE@">sort</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @PREPARE_ENV@ #set temp_dir = 'tmp' mkdir $temp_dir && bcftools @EXECUTABLE@ $input_file --output-file '$output_file' @OUTPUT_TYPE@ --temp-dir '$temp_dir' ]]> </command> <inputs> <expand macro="macro_input"/> <expand macro="macro_select_output_type"/> </inputs> <outputs> <expand macro="macro_vcf_output"/> </outputs> <tests> <test> <param name="input_file" value="unsorted.vcf" ftype="vcf"/> <param name="output_type" value="v"/> <output name="output_file" file="sorted.vcf" ftype="vcf"/> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ ===================================== Sort VCF/BCF files. @BCFTOOLS_MANPAGE@#@EXECUTABLE@ @BCFTOOLS_WIKI@ ]]> </help> <expand macro="citations"/> </tool>