comparison emboss_syco.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: syco96" name="syco" version="5.0.0">
  <!-- graphics output -->
  <description>Synonymous codon usage Gribskov statistic plot</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
  -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="cfile" type="select">
      <label>Codon Usage File</label>
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eyeastcai.cut">Eyeastcai.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="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="window" type="text" value="30">
      <label>Averaging window</label>
    </param>
    <param name="uncommon" type="select">
      <label>Show common codon usage</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="minimum" type="text" value="0.15">
      <label>Minimum value for a common codon</label>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="ofile1" />
    <data format="syco" name="ofile2" />
  </outputs>
 <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="cfile" value="Ehum.cut"/>

      <param name="minimum" value="0.15"/>
      <output name="ofile2" file="emboss_syco_out.syco"/>
    </test>
  </tests> -->
  <help>

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.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: syco96" name="syco" version="5.0.0.1">
  <!-- graphics output -->
  <description>Synonymous codon usage Gribskov statistic plot</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' syco -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -cfile $cfile -window $window -uncommon $uncommon -minimum $minimum
  -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence" />
    <param name="cfile" type="select" label="Codon usage file">
      <option value="Ehum.cut">Ehum.cut</option>
      <option value="Eyeastcai.cut">Eyeastcai.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="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="window" type="integer" value="30" label="Averaging window" />
    <param name="uncommon" type="select" label="Show common codon usage">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="minimum" type="float" value="0.15" label="Minimum value for a common codon" />
  </inputs>
  <outputs>
    <data name="ofile1" format="png" />
    <data name="ofile2" format="syco" />
  </outputs>
 <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="cfile" value="Ehum.cut"/>

      <param name="minimum" value="0.15"/>
      <output name="ofile2" file="emboss_syco_out.syco"/>
    </test>
  </tests> -->
  <help>
    You can view the original documentation here_.

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