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<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.

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

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**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>