<tool id="matrix2qgene" name="Matrix to QGene">
  <description>file format conversion</description>
  <command interpreter="perl">matrix2qgene.pl $matrix $output $map $header $trait</command>
  <inputs>
    <param format="tabular" name="matrix" type="data" label="Matrix file"></param>
    <param format="tabular" name="map" type="data" label="Physical Map file"></param>
    <param format="tabular" name="header" type="data" label="Header file"></param>
    <param format="tabular" name="trait" type="data" label="Trait file"></param>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="${matrix.name} QGene format"/>
  </outputs>

  <tests>
    <test>
      <output name="out1" file="${matrix}.qdf"/>
    </test>
  </tests>

  <help>
This tool converts a SNP matrix file to QGene file format.
  </help>

</tool>