comparison emboss_codcmp.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: codcmp12" name="codcmp" version="5.0.0">
  <description>Codon usage table comparison</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command>
  <inputs>
    <param name="cfile1" type="select">
      <label>Codon Usage File 1</label>
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eacc.cut">Eacc.cut</option>
      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
      <option value="Eaidlav.cut">Eaidlav.cut</option>

      <option value="Eyscmt.cut">Eyscmt.cut</option>
      <option value="Eysp.cut">Eysp.cut</option>
      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
      <option value="Ezma.cut">Ezma.cut</option>
    </param>
    <param name="cfile2" type="select">
      <label>Codon Usage File 2</label>
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eacc.cut">Eacc.cut</option>
      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
      <option value="Eaidlav.cut">Eaidlav.cut</option>

      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
      <option value="Ezma.cut">Ezma.cut</option>
    </param>
  </inputs>
  <outputs>
    <data format="codcmp" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="cfile1" value="Ehum.cut"/>
      <param name="cfile2" value="Eacc.cut"/>
      <output name="out_file1" file="emboss_codcmp_out.codcmp"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.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: codcmp12" name="codcmp" version="5.0.0">
  <description>Codon usage table comparison</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>codcmp -first $cfile1 -second $cfile2 -outfile '$out_file1' -auto</command>
  <inputs>
    <param name="cfile1" type="select" label="Codon usage file 1">
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eacc.cut">Eacc.cut</option>
      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
      <option value="Eaidlav.cut">Eaidlav.cut</option>

      <option value="Eyscmt.cut">Eyscmt.cut</option>
      <option value="Eysp.cut">Eysp.cut</option>
      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
      <option value="Ezma.cut">Ezma.cut</option>
    </param>
    <param name="cfile2" type="select" label="Codon usage file 2">
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eacc.cut">Eacc.cut</option>
      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
      <option value="Eaidlav.cut">Eaidlav.cut</option>

      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
      <option value="Ezma.cut">Ezma.cut</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="codcmp" />
  </outputs>
  <tests>
    <test>
      <param name="cfile1" value="Ehum.cut"/>
      <param name="cfile2" value="Eacc.cut"/>
      <output name="out_file1" file="emboss_codcmp_out.codcmp"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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