comparison emboss_oddcomp.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
  <!-- output contains file location info, commented out functional tests -->
  <description>Find protein sequence regions with a biased composition</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
    </param>
    <param name="window" type="text" value="30">
      <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
    </param>
    <param name="ignorebz" type="select">
      <label>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</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data format="oddcomp" name="out_file1" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="emboss_compseq_out.compseq"/>

      <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
    </test>
  </tests> -->
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.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>

11:0e2484b6829b

<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1">
  <!-- 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"/>

      <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>