<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
  <!-- puts file information in output report -->
  <description>Match large sequences against one or more other sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
  $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Large sequences</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Sequences to match</label>
    </param>
    <param name="gapopen" size="4" type="text" value="10.0">
      <label>Gap opening penalty</label>
    </param>
    <param name="gapextend" size="4" type="text" value="0.5">
      <label>Gap extension penalty</label>
    </param>
    <param name="width" size="4" type="text" value="16">
      <label>Alignment width</label>
    </param>
    <param name="wordlen" size="4" type="text" value="6">
      <label>Word length for initial matching</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Alignment File Format</label>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>
      <option value="pair">Pair (p)</option>
      <option value="markx0">Markx0 (p)</option>
      <option value="markx1">Markx1 (p)</option>
      <option value="markx2">Markx2 (p)</option>
      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
  </inputs>
  <outputs>
    <data format="simple" name="ofile1" />
    <data format="supermatcher" name="ofile2" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="gapopen" value="10.0"/>
      <param name="gapextend" value="0.5"/>
      <param name="width" value="16"/>
      <param name="wordlen" value="6"/>
      <param name="out_format1" value="fasta"/>
      <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
    </test>
  </tests> -->
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html
  </help>
</tool>