<tool id="EMBOSS: plotorf76" name="plotorf" version="5.0.0">

  <!-- produces png file output -->
  <description>Plot potential open reading frames</description>

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

  <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>

  <inputs>

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

      <label>Sequence</label>

    </param>

    <param name="start" size="15" type="text" value="ATG">

      <label>Start codons</label>

    </param>

    <param name="stop" size="15" type="text" value="TAA">

      <label>Stop codons</label>

    </param>

  </inputs>

  <outputs>

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

  </outputs>
  <!--  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="start" value="ATG"/>
      <param name="stop" value="TAA"/>
      <output name="out_file1" file="emboss_plotorf_out.png"/>
    </test>
  </tests> -->

  <help>

.. class:: warningmark

The input dataset needs to be sequences.

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