view vcfsort.xml @ 4:694dfc3f5d45 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit 9a0c41967765d120a8fc519c0c7f09cbe3a6efbe"

<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0">
    <description>Sort VCF dataset by coordinate</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="8.31">coreutils</requirement>
    </requirements>
    <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>