Mercurial > repos > devteam > vcfsort
changeset 3:5b7120c66efc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
| author | iuc |
|---|---|
| date | Mon, 26 Mar 2018 12:28:53 -0400 |
| parents | a8c5440d69e3 |
| children | f0580efedada |
| files | vcfsort.xml |
| diffstat | 1 files changed, 21 insertions(+), 21 deletions(-) [+] |
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--- a/vcfsort.xml Mon Oct 03 11:23:06 2016 -0400 +++ b/vcfsort.xml Mon Mar 26 12:28:53 2018 -0400 @@ -1,23 +1,24 @@ -<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@.0"> - <description>Sort VCF dataset by coordinate</description> - <macros> - <import>macros.xml</import> - </macros> - <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input1" value="vcfsort-test1-input.vcf"/> - <output name="out_file1" file="vcfsort-test1.vcf"/> - </test> +<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0"> + <description>Sort VCF dataset by coordinate</description> + <macros> + <import>macros.xml</import> + </macros> + <command><![CDATA[ +(grep ^"#" "${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> - + <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 @@ -25,6 +26,5 @@ .. 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> + </help> </tool>