view emboss_merger.xml @ 17:bde3097ac0f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit d5dfff2cd58b094e0e4a6f8dc475de5facd9700b"

<tool id="EMBOSS: merger54" name="merger" version="@VERSION@.1">
  <description>Merge two overlapping nucleic acid sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence 1" />
    <param name="input2" type="data" format="data" label="Sequence 2" />
    <param name="gapopen" type="float" value="50.0" label="Gap opening penalty" />
    <param name="gapextend" type="float" value="5.0" label="Gap extension penalty" />
    <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>
    <param name="out_format2" type="select" label="Output alignment file format">
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>
      <option value="pair">Pair (p)</option>
      <option value="markx0">Markx0 (p)</option>
      <option value="markx1">Markx1 (p)</option>
      <option value="markx2">Markx2 (p)</option>
      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fasta" />
    <data name="out_file2" format="simple" />
  </outputs>
  <help>
    You can view the original documentation here_.

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