<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
  <description>Non-overlapping wordmatch dotplot of two sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <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>