root/galaxy-central/tools/emboss_5/emboss_cai_custom.xml

<tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0">
  <description>CAI codon adaptation index using custom codon usage file</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param format="txt" name="input2" type="data">
      <label>Codon Usage File</label>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="out_file1" />
  </outputs>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html
  </help>
</tool>