view emboss_compseq.xml @ 20:21a9fb508031 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

<tool id="EMBOSS: compseq14" name="compseq" version="@VERSION@.1">
  <description>Count composition of dimer/trimer/etc words in a sequence</description>
  <expand macro="bio_tools" />
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>compseq -sequence '$input1' -outfile '$out_file1' -word $word -frame $frame -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="On query" />
    <param name="word" type="integer" value="2" label="Size of word (window) to count" />
    <param name="frame" type="select" label="Frame to inspect">
      <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 name="out_file1" format="compseq" />
  </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://galaxy-iuc.github.io/emboss-5.0-docs/compseq.html
  </help>
  <expand macro="citations" />
</tool>