<tool id="alchemy2matrix" name="Alchemy to Matrix">
  <description>file converter</description>
  <command interpreter="perl">alchemy2matrix.pl $input $output</command>
  <inputs>
    <param format="tabular" name="input" type="data" label="Source file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="raw_data.txt"/>
      <output name="out_file1" file="output.txt"/>
    </test>
  </tests>

  <help>
This tool converts an alchemy-output file format to a SNP matrix format.
  </help>

</tool>