annotate glang-galaxy-conf/kbws/kkalign.xml @ 2:8947fca5f715 draft default tip

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<tool id="EMBOSS: kkalign" name="kkalign" version="1.0.2">
  <description>Multiple sequence alignment using Kalign</description>
  <command>kkalign -seqall $input1 -moltype $moltype -gpo $gpo -gpe $gpe -tgpe $tgpe -bonus $bonus -auto -outfile $out_file1</command>
  <inputs>
  <param format="data" name="input1" type="data">
    <label>Sequence</label>
  </param>
    <param name="moltype" size="4" type="text" value="auto">
      <label>Molecular (sequence) type. 'auto' (auto detection by input sequence), 'N'(nucleotide) or 'P'(protein)</label>
    </param>
    <param name="gpo" size="4" type="float" value="">
      <label>gap creation penalty</label>
    </param>
    <param name="gpe" size="4" type="float" value="">
      <label>gap extension penalty</label>
    </param>
    <param name="tgpe" size="4" type="float" value="">
      <label>terminal gap penalty</label>
    </param>
    <param name="bonus" size="4" type="float" value="">
      <label>bonus score</label>
    </param>

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