<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1">
  <!-- produces png file, not added functional tests -->
  <description>Displays all-against-all dotplots of a set of sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
  $gap -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence" />
    <param name="wordsize" type="integer" value="6" label="Word size" />
    <param name="boxit" type="select" label="Draw a box around each dotplot">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="gap" type="integer" value="10" label="Size of gap" />
  </inputs>
  <outputs>
    <data name="output1" format="polydot" />
    <data name="output2" format="png" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="wordsize" value="6"/>
      <param name="boxit" value="yes"/>
      <param name="gap" value="10"/>
      <output name="output1" file="emboss_polydot_out.png"/>
    </test>
  </tests>-->
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

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