<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



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**Citation**



If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>