annotate emboss_5/emboss_pepwindow.xml @ 5:2cf967772a40

Fix for emboss_format_corrector.py. Datatypes should be changed before the job is run.

<tool id="EMBOSS: pepwindow73" name="pepwindow" version="5.0.0">
  <!-- produces png file -->
  <description>Displays protein hydropathy</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="length" size="10" type="text" value="7">
      <label>Window size</label>
    </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/pepwindow.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>