<tool id="EMBOSS: dotpath25" name="dotpath" version="@VERSION@.1">
  <description>Non-overlapping wordmatch dotplot of two sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence 1" />
    <param name="input2" type="data" format="data" label="Sequence 2" />
    <param name="wordsize" type="integer" min="2" value="4" label="Word size" />
    <param name="overlaps" type="select" label="Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="boxit" type="select" label="Draw a box around dotplot">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="png" />
  </outputs>
  <!-- functional tests not possible since image output contains file name information and timestamp -->
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dotpath.html
  </help>
  <expand macro="citations" />
</tool>