<tool id="EMBOSS: merger54" name="merger" version="5.0.0">

  <description>Merge two overlapping nucleic acid sequences</description>

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

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

      <label>Sequence 1</label>

    </param>

    <param format="data" name="input2" type="data">

      <label>Sequence 2</label>

    </param>

    <param name="gapopen" size="4" type="text" value="50.0">

      <label>Gap opening penalty</label>

    </param>

    <param name="gapextend" size="4" type="text" value="5.0">

      <label>Gap extension penalty</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>

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

      <label>Output Alignment File Format</label>

      <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 format="fasta" name="out_file1" />

    <data format="simple" name="out_file2" />

  </outputs>

  <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/merger.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>