Mercurial > repos > greg > bcftools_sort
diff bcftools_sort.xml @ 0:1d4c51dcbbbe draft
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author | greg |
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date | Wed, 19 Dec 2018 08:58:27 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_sort.xml Wed Dec 19 08:58:27 2018 -0500 @@ -0,0 +1,47 @@ +<?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>