<tool id="codon_usage" name="Codon Usage" version="0.1.0">
  <description>for each sequence in a file</description>
  <requirements>
    <requirement type=“package” version=“2.7.10”>python</requirement>
    <requirement type=“package” version=“1.72”>biopython</requirement>
    <requirement type=“package” version=“0.23.4”>pandas</requirement>
  </requirements> 
  
  <command>codon_usage.py -i $input -t $input_type -o $output -c $codon_table</command>
  <inputs>
    <param name="input" format="fasta" type="data" label="Source file"/>

    <param name="input_type" type="select" format="text">
			<label>Indicate the input file format</label>
				<option value="fasta">Fasta</option>
				<option value="gbk">gbk</option>
		</param>

    <param name="codon_table" type="select" format="text">
			<label>Choose the proper codon table for your organism)</label>
        <option value="Archaeal"> Archaeal</option>
        <option value="Bacterial">Bacterial</option>
        <option value="Standard">Standard</option>
        
		</param>

  </inputs>



  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>

  <help>
This tool compute codon usage of an annotated genome [preferably Prokaryotes].
  </help>
</tool>