view emboss_vectorstrip.xml @ 20:21a9fb508031 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="@VERSION@.1">
  <description>Strips out DNA between a pair of vector sequences</description>
  <expand macro="bio_tools" />
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <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 name="input1" type="data" format="fasta" label="Sequences" />
    <param name="input2" type="data" format="data" label="Vector file" />
    <param name="mismatch" type="integer" value="10" label="Max allowed percent mismatch" />
    <param name="besthits" type="select" label="Show only the best hits (minimize mismatches)">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="linkera" type="text" value="" label="The 5' sequence" />
    <param name="linkerb" type="text" value="" label="The 3' sequence" />
    <param name="out_format1" type="select" label="Output sequence file format">
      <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 name="ofile1" format="fasta" />
    <data name="ofile2" format="vectorstrip" />
  </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> -->
  <help>
    You can view the original documentation here_.

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