annotate emboss_5/emboss_plotorf.xml @ 8:b810c96613ee draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

<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" type="text" value="ATG">
      <label>Start codons</label>
    </param>
    <param name="stop" 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.

-----

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

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

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>