root/galaxy-central/tools/emboss_5/emboss_dotmatcher.xml

<tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0">
  <description>Displays a thresholded dotplot of two sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph 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="windowsize" size="4" type="text" value="10">
      <label>Window size</label>
    </param>
    <param name="threshold" size="4" type="text" value="23">
      <label>Threshold</label>
    </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/dotmatcher.html
  </help>
</tool>