view emboss_etandem.xml @ 10:9b98d3d903c6 draft

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

<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
  <description>Looks for tandem repeats in a nucleotide sequence</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="minrepeat" type="text" value="10">
      <label>Minimum repeat size</label>
    </param>
    <param name="maxrepeat" type="text" value="10">
      <label>Maximum repeat size</label>
    </param>
    <param name="threshold" type="text" value="20">
      <label>Threshold score</label>
    </param>
    <param name="mismatch" type="select">
      <label>Allow N as a mismatch</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="uniform" type="select">
      <label>Allow uniform consensus</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Report File Format</label>
      <option value="table">Table</option>
      <option value="embl">EMBL</option>
      <option value="genbank">GENBANK</option>
      <option value="gff">GFF</option>
      <option value="pir">PIR</option>
      <option value="swiss">SwissProt</option>
      <option value="dbmotif">DbMotif</option>
      <option value="diffseq">Diffseq</option>
      <option value="excel">Excel (tab delimited)</option>
      <option value="feattable">FeatTable</option>
      <option value="motif">Motif</option>
      <option value="regions">Regions</option>
      <option value="seqtable">SeqTable</option>
      <option value="simple">SRS Simple</option>
      <option value="srs">SRS</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data format="etandem" name="out_file1" />
    <data format="table" name="ofile2" />    
  </outputs>
    <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="minrepeat" value="10"/>
      <param name="maxrepeat" value="10"/>
      <param name="threshold" value="20"/>
      <param name="mismatch" value="no"/>
       <param name="uniform" value="no"/>
      <param name="out_format1" value="table"/>
      <output name="ofile2" file="emboss_etandem_out.table"/>
    </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/etandem.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>