/tools/emboss_5/emboss_sirna.xml

<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">

  <description>Finds siRNA duplexes in mRNA</description>

  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>

  <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2

  -auto</command>

  <inputs>

    <param format="fasta" name="input1" type="data">

      <label>Sequences</label>

    </param>

    <param name="poliii" type="select">

      <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="aa" type="select">

      <label>Select only those 23 base regions that start with AA</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="tt" type="select">

      <label>Select only those 23 base regions that end with TT</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="polybase" type="select">

      <label>Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row</label>

      <option value="yes">Yes</option>

      <option value="no">No</option>

    </param>

    <param name="context" type="select">

      <label>Displays the whole 23 bases of the region with the first two bases in brackets</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>

    <param name="out_format2" type="select">

      <label>Output Sequence File Format</label>

      <option value="fasta">FASTA (m)</option>

      <option value="acedb">ACeDB (m)</option>

      <option value="asn1">ASN.1 (m)</option>

      <option value="clustal">Clustal (m)</option>

      <option value="codata">CODATA (m)</option>

      <option value="embl">EMBL (m)</option>

      <option value="fitch">Fitch (m)</option>

      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>

      <option value="genbank">GENBANK (m)</option>

      <option value="gff">GFF (m)</option>

      <option value="hennig86">Hennig86 (m)</option>

      <option value="ig">Intelligenetics (m)</option>

      <option value="jackknifer">Jackknifer (m)</option>

      <option value="jackknifernon">Jackknifernon (m)</option>

      <option value="mega">Mega (m)</option>

      <option value="meganon">Meganon (m)</option>

      <option value="msf">Wisconsin Package GCG's MSF (m)</option>

      <option value="pir">NBRF (PIR) (m)</option>

      <option value="ncbi">NCBI style FASTA (m)</option>

      <option value="nexus">Nexus/PAUP (m)</option>

      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>

      <option value="phylip">PHYLIP interleaved (m)</option>

      <option value="phylipnon">PHYLIP non-interleaved (m)</option>

      <option value="selex">SELEX (m)</option>

      <option value="staden">Staden (s)</option>

      <option value="strider">DNA strider (m)</option>

      <option value="swiss">SwisProt entry (m)</option>

      <option value="text">Plain sequence (s)</option>

      <option value="treecon">Treecon (m)</option>

    </param>

  </inputs>

  <outputs>

    <data format="table" name="ofile1" />

    <data format="fasta" name="ofile2" />

  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="poliii" value="no"/>
      <param name="aa" value="no"/>
      <param name="tt" value="no"/>
      <param name="polybase" value="yes"/>
      <param name="context" value="no"/>
      <param name="mismatchpercent" value="0"/>
      <param name="out_format1" value="gff"/>
      <param name="out_format2" value="fasta"/>
      <output name="ofile2" file="emboss_sirna_out.fasta"/>
    </test>
  </tests>

  <code file="emboss_format_corrector.py" />

  <help>

.. class:: warningmark

The input dataset needs to be sequences.

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



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**Citation**



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>