<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">

  <!-- output contains file location info, commented out functional tests -->
  <description>Find protein sequence regions with a biased composition</description>

  <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>

  <inputs>

    <param format="data" name="input1" type="data">

      <label>Sequences</label>

    </param>

    <param format="data" name="input2" type="data">

      <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>

    </param>

    <param name="window" size="4" type="text" value="30">

      <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>

    </param>

    <param name="ignorebz" type="select">

      <label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words

      containing them, just noting them in the count of 'Other' words</label>

      <option value="yes">Yes</option>

      <option value="no">No</option>

    </param>

  </inputs>

  <outputs>

    <data format="oddcomp" name="out_file1" />

  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="emboss_compseq_out.compseq"/>
      <param name="window" value="30"/>
      <param name="ignorebz" value="yes"/>
      <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
    </test>
  </tests> -->

  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html
  </help>
</tool>