/tools/emboss_5/emboss_dotpath.xml

<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">

  <description>Non-overlapping wordmatch dotplot of two sequences</description>

  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png

  -auto</command>

  <inputs>

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

      <label>Sequence 1</label>

    </param>

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

      <label>Sequence 2</label>

    </param>

    <param name="wordsize" size="4" type="text" value="4">

      <label>Word size (Integer 2 or more)</label>

    </param>

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

      <label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label>

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

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

    </param>

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

      <label>Draw a box around dotplot</label>

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

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

    </param>

  </inputs>

  <outputs>

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

  </outputs>
  <!-- functional tests not possible since image output contains file name information and timestamp -->

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