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

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<tool id="EMBOSS: ggcsi" name="ggcsi" version="1.0.2">
  <description>GC Skew Index: an index for strand-specific mutational bias</description>
  <command>ggcsi -sequence $input1 -gcsi $gcsi -window $window -purine $purine -keto $keto -at $at -pval $pval -auto -noaccid -outfile $out_file1</command>
  <inputs>
  <param format="data" name="input1" type="data">
    <label>Sequence</label>
  </param>
    <param name="gcsi" type="select" value="2">
      <label>GCSI version to use</label>
      <option value="1">1</option>
      <option value="2">2</option>
    </param>
    <param name="window" size="4" type="integer" value="4096">
      <label>Number of windows. Must be a power of 2</label>
    </param>
    <param name="purine" type="select" value="no">
      <label>Use purine skew for calculation</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="keto" type="select" value="no">
      <label>Use keto skew for calculation</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="at" type="select" value="no">
      <label>Use AT skew for calculation</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="pval" type="select" value="no">
      <label>Calculate p-value when GCSI version 2 is selected</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>

  </inputs>
  <outputs>
    <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />    
  </outputs>
</tool>