view emboss_oddcomp.xml @ 14:27c43fb015f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: oddcomp64" name="oddcomp" version="@VERSION@.1">
  <!-- output contains file location info, commented out functional tests -->
  <description>Find protein sequence regions with a biased composition</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequences" />
    <param name="input2" type="data" format="data" label="Dataset in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis" />
    <param name="window" type="integer" value="30" label="Size of window in which to count" help="If you want to count frequencies in a 40 aa stretch you should enter 40 here" />
    <param name="ignorebz" type="select" label="Ignore B and Z" help="The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="oddcomp" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="emboss_compseq_out.compseq"/>
      <param name="window" value="30"/>
      <param name="ignorebz" value="yes"/>
      <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
    </test>
  </tests> -->
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/oddcomp.html
  </help>
  <expand macro="citations" />
</tool>