<tool id="EMBOSS: octanol63" name="octanol" version="5.0.0">
  <!-- graphics output with filename, no functional tests added -->  

  <description>Displays protein hydropathy</description>

  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>

  <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot

  -differenceplot $differenceplot -auto</command>

  <inputs>

    <param format="data" name="input1" type="data">

      <label>Sequences</label>

    </param>

    <param name="width" size="4" type="text" value="19">

      <label>Window size</label>

    </param>

    <param name="octanolplot" type="select">

      <label>Display the octanol plot</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="interfaceplot" type="select">

      <label>Display the interface plot</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="differenceplot" type="select">

      <label>Display the difference plot</label>

      <option value="yes">Yes</option>

      <option value="no">No</option>

    </param>

  </inputs>

  <outputs>

    <data format="png" name="out_file1" />

  </outputs>

  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.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>