Mercurial > repos > devteam > vcfsort
view vcfsort.xml @ 2:d92d6f631ff5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author | iuc |
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date | Mon, 26 Mar 2018 12:16:24 -0400 |
parents | 586f4536fc65 |
children | 24f96edb5b29 |
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<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0"> <description>Sort VCF dataset by coordinate</description> <macros> <import>macros.xml</import> </macros> <command><![CDATA[ (grep ^"#" "${input1}" && grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}" ]]></command> <inputs> <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> </inputs> <outputs> <data format="vcf" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="vcfsort-test1-input.vcf"/> <output name="out_file1" file="vcfsort-test1.vcf"/> </test> </tests> <help> This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file .. class:: infomark The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). </help> </tool>