<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0">

  <description>Finds neighbouring pairs of features in sequences</description>

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

  <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"

  -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap

  -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>

  <inputs>

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

      <label>Sequences</label>

    </param>

    <param name="atype" size="50" type="text" value="*">

      <label>Feature type you wish to allow. Feature 1</label>

    </param>

    <param name="btype" size="50" type="text" value="*">

      <label>Feature type you wish to allow. Feature 2</label>

    </param>

    <param name="minrange" size="5" type="text" value="0">

      <label>Minimun range</label>

    </param>

    <param name="maxrange" size="5" type="text" value="0">

      <label>Maximum range</label>

    </param>

    <param name="asource" size="50" type="text" value="*">

      <label>Feature source 1</label>

    </param>

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

      <label>Feature sense 1</label>

      <option value="0">Any sense</option>

      <option value="+">Forward sense</option>

      <option value="-">Reverse sense</option>

    </param>

    <param name="aminscore" size="5" type="text" value="0.0">

      <label>Feature 1 minimum score</label>

    </param>

    <param name="amaxscore" size="5" type="text" value="0.0">

      <label>Feature1 maxiumum score</label>

    </param>

    <param name="atag" size="50" type="text" value="*">

      <label>Feature 1 tag</label>

    </param>

    <param name="avalue" size="50" type="text" value="*">

      <label>Tag 1 value</label>

    </param>

    <param name="bsource" size="50" type="text" value="*">

      <label>Feature 2 source</label>

    </param>

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

      <label>Feature 2 sense</label>

      <option value="0">Any sense</option>

      <option value="+">Forward sense</option>

      <option value="-">Reverse sense</option>

    </param>

    <param name="bminscore" size="5" type="text" value="0.0">

      <label>Feature 2 miniumum score</label>

    </param>

    <param name="bmaxscore" size="5" type="text" value="0.0">

      <label>Feature 2 maximum score</label>

    </param>

    <param name="btag" size="50" type="text" value="*">

      <label>Feature 2 tag</label>

    </param>

    <param name="bvalue" size="50" type="text" value="*">

      <label>Feature 2 tag value</label>

    </param>

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

      <label>opverlaps allowed</label>

      <option value="A">Any</option>

      <option value="O">Overlap required but not within</option>

      <option value="NO">No overlaps are allowed</option>

      <option value="NW:">Overlap required but not within</option>

      <option value="AW">A must be all within B</option>

      <option value="BW">B must be all within A</option>

    </param>

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

      <label>How to determine range</label>

      <option value="N">From nearest ends</option>

      <option value="L">From left ends</option>

      <option value="R">From right ends</option>

      <option value="F">From furthest ends</option>

    </param>

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

      <label>Required sense</label>

      <option value="A">Any sense</option>

      <option value="S">Same sense</option>

      <option value="O">Opposite sense</option>

    </param>

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

      <label>Required order of the two features</label>

      <option value="A">Any</option>

      <option value="AB">Feature A then feature B</option>

      <option value="BA">Feature B then feature A</option>

    </param>

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

      <label>Write out the two features themselves</label>

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

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

    </param>

    <param name="typeout" size="50" type="text" value="misc_feature">

      <label>New feature type</label>

    </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>

  </inputs>

  <outputs>

    <data format="table" name="out_file1" />

  </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/twofeat.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>