annotate emboss_5/emboss_compseq.xml @ 8:b810c96613ee draft

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

<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
  <description>Count composition of dimer/trimer/etc words in a sequence</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="word" type="text" value="2">
      <label>Size of word (window) to count</label>
    </param>
    <param name="frame" type="select">
      <label>Frame to inspect</label>
      <option value="0">All Frames</option>
      <option value="1">Frame 1</option>
      <option value="2">Frame 2</option>
      <option value="3">Frame 3</option>
    </param>
  </inputs>
  <outputs>
    <data format="compseq" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="word" value="2"/>
      <param name="frame" value="0"/>
      <output name="out_file1" file="emboss_compseq_out.compseq"/>
    </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/compseq.html

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**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>