view vcfsort.xml @ 0:433d50620231 draft

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<tool id="vcfsort" name="VCFsort:" version="0.0.2">
  <description>Sort VCF dataset by coordinate</description>
  <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>
    </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>