view emboss_cpgreport.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
  <description>Reports all CpG rich regions</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command><![CDATA[
    cpgreport 
      -sequence '$input1' 
      -outfile '$out_file1' 
      -outfeat '$out_file2'
      -offormat3 '$out_format2'
      -score '$score'
      -auto
  ]]>
  </command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="score" type="text" value="17">
      <label>Score for each CG sequence found (1-200)</label>
    </param>
    <param name="out_format2" type="select" label="Output Feature File Format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data format="cpgreport" name="out_file1" />
    <data format="gff" name="out_file2" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="score" value="17"/>
      <param name="out_format2" value="embl"/>
      <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
    </test>
    <!-- <test>
      <param name="input1" value="2.fasta"/>
      <param name="score" value="17"/>
      <param name="out_format2" value="gff"/>
      <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
    </test>  -->
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.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>