view vcfdistance.xml @ 1:815622f17a3d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfdistance commit 0b9b6512272b82637c2f1e831367e89aed77ae79

<tool id="vcfdistance" name="VCFdistance:" version="@WRAPPER_VERSION@.0">
  <description>Calculate distance to the nearest variant</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio" />
  <command>cat "${input1}" | vcfdistance > "${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="vcflib.vcf"/>
      <output name="out_file1" file="vcfdistance-test1.vcf"/>
    </test>
    </tests>
  <help>

Adds a value to each VCF record indicating the distance to the nearest variant in the file.

.. class:: infomark

The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).

----

Vcfdistance @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>