root/galaxy-central/tools/emboss_5/emboss_vectorstrip.xml @ 3

<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
  <description>Strips out DNA between a pair of vector sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
  "$linkerb" -osformat4 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Vector file</label>
    </param>
    <param name="mismatch" size="4" type="text" value="10">
      <label>Max allowed percent mismatch</label>
    </param>
    <param name="besthits" type="select">
      <label>Show only the best hits (minimize mismatches)</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="linkera" size="50" type="text" value="">
      <label>The 5' sequence</label>
    </param>
    <param name="linkerb" size="50" type="text" value="">
      <label>The 3' sequence</label>
    </param>
    <param name="out_format1" 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="fasta" name="ofile1" />
    <data format="vectorstrip" name="ofile2" />
  </outputs>
  <!--  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="input2" value="2.fasta"/>
      <param name="mismatch" value="10"/>
      <param name="besthits" value="yes"/>
      <param name="linkera" value=""/>
      <param name="linkerb" value=""/>
      <param name="out_format1" value="fasta"/>
      <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
    </test>
  </tests> -->
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html
  </help>
</tool>