view glang-galaxy-conf/gembassy/ggeneskew.xml @ 2:8947fca5f715 draft default tip

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<tool id="EMBOSS: ggeneskew" name="ggeneskew" version="1.0.2">
  <description>Calculates and plots the gene strand bias of the given genome</description>
  <command interpreter="perl">gembassy_calcandplot_wrapper.pl ggeneskew -sequence $input1 -window $window -slide $slide -cumulative $cumulative -base $base -gctri $gctri -auto -noaccid $out_file1 $out_file2</command>
  <inputs>
  <param format="data" name="input1" type="data">
    <label>Sequence</label>
  </param>
    <param name="window" size="4" type="integer" value="10000">
      <label>Window size to observe</label>
    </param>
    <param name="slide" size="4" type="integer" value="10000">
      <label>Window slide size</label>
    </param>
    <param name="cumulative" type="select" value="no">
      <label>Input 1 to calculate cumulative skew</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="base" type="select" value="none">
      <label>Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews</label>
      <option value="none">None</option>
      <option value="gc">Gc</option>
      <option value="at">At</option>
      <option value="purine">Purine</option>
      <option value="keto">Keto</option>
    </param>
    <param name="gctri" type="select" value="no">
      <label>Include to use only the third codon positions</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>

  </inputs>
  <outputs>
    <data format="csv" name="out_file1" label="${tool.name} data for ${input1.name}" />
    <data format="png" name="out_file2" label="${tool.name} plot for ${input1.name}" />    
  </outputs>
</tool>