<tool id="dnds" name="dNdS Report" version="0.1.0">
    <description>Calculate the dN/dS value for each region in a bed file</description>
    <requirements>
          <requirement type="package" version="0.2.3">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools dnds $csv_file $ref_file $offset -o output.csv

    ]]></command>
    <inputs>
        <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" />
        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
        <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
    <tests>
        <test>
            <param name="csv_file" value="mutant_types.csv" />
            <param name="ref_file" value="hxb2_pol.fas" />
            <output name="output" ftype="csv" >
                <assert_contents>
                    <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/>
                    <has_text text="RT,0.0334,0.0111,1,1,3.0539" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

dNdS Report
===================

Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants).

    ]]></help>
    <citations>
    </citations>
</tool>