view emboss_twofeat.xml @ 12:ace31bbde4c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9d484642914b581ce35f254466b849d3c4c2c06c

<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1">
  <description>Finds neighbouring pairs of features in sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <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 name="input1" type="data" format="data" label="Sequences" />
    <param name="atype" type="text" value="*" label="Feature type you wish to allow. Feature 1" />
    <param name="btype" type="text" value="*" label="Feature type you wish to allow. Feature 2" />
    <param name="minrange" type="integer" value="0" label="Minimun range" />
    <param name="maxrange" type="integer" value="0" label="Maximum range" />
    <param name="asource" type="text" value="*" label="Feature source 1" />
    <param name="asense" type="select" label="Feature sense 1">
      <option value="0">Any sense</option>
      <option value="+">Forward sense</option>
      <option value="-">Reverse sense</option>
    </param>
    <param name="aminscore" type="float" value="0.0" label="Feature 1 minimum score" />
    <param name="amaxscore" type="float" value="0.0" label="Feature1 maximum score" />
    <param name="atag" type="text" value="*" label="Feature 1 tags" />
    <param name="avalue" type="text" value="*" label="Feature 1 tag values" />
    <param name="bsource" type="text" value="*" label="Feature 2 source" />
    <param name="bsense" type="select" label="Feature 2 sense">
      <option value="0">Any sense</option>
      <option value="+">Forward sense</option>
      <option value="-">Reverse sense</option>
    </param>
    <param name="bminscore" type="float" value="0.0" label="Feature 2 minimum score" />
    <param name="bmaxscore" type="float" value="0.0" label="Feature 2 maximum score" />
    <param name="btag" type="text" value="*" label="Feature 2 tags" />
    <param name="bvalue" type="text" value="*" label="Feature 2 tag values" />
    <param name="overlap" type="select" label="Allowed overlaps">
      <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">
      <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">
      <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">
      <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">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="typeout" type="text" value="misc_feature" label="New feature type" />
    <param name="out_format1" type="select" label="Output report file format">
      <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 name="out_file1" format="table" />
  </outputs>
  <help>
    You can view the original documentation here_.

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