view tools/emboss_5/emboss_compseq.xml @ 1:cdcb0ce84a1b

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<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" size="4" 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.

-----

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