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

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<tool id="EMBOSS: gbasezvalue" name="gbasezvalue" version="1.0.2">
  <description>Extracts conserved oligomers per position using Z-score</description>
  <command>gbasezvalue -sequence $input1 -limit $limit -position $position -patlen $patlen -upstream $upstream -downstream $downstream -auto -noaccid -outfile $out_file1</command>
  <inputs>
  <param format="data" name="input1" type="data">
    <label>Sequence</label>
  </param>
    <param name="limit" size="4" type="integer" value="5">
      <label>Rank threshold for showing the conserved oligomer</label>
    </param>
    <param name="position" type="select" value="start">
      <label>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</label>
      <option value="start">Start</option>
      <option value="end">End</option>
    </param>
    <param name="patlen" size="4" type="integer" value="3">
      <label>Length of oligomer to count</label>
    </param>
    <param name="upstream" size="4" type="integer" value="30">
      <label>Length upstream of specified position to create PWM</label>
    </param>
    <param name="downstream" size="4" type="integer" value="30">
      <label>Length downstream of specified position to create PWM</label>
    </param>

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