<tool id="callcodonvar" name="Codon Variants" version="0.7.0">
    <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
    <requirements>
          <requirement type="package" version="0.7.0">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        cat $input_genes &&

        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
        quasitools call codonvar $input_bam $ref_file $offset $input_genes

		#if $var_file:
			$var_file 
		#end if

        #if $error_rate:
            -e $error_rate
        #end if

        -o output.csv

    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" optional="false" label="Bam 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"/>
        <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
		<param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021." />
		<param name="var_file" type="data" format="vcf" optional="true" label="Variants file" help="Not required. If not supplied, a variants file will be generated using the input bam file." />
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="align.bam" />
            <param name="ref_file" value="hxb2_pol.fas" />
            <param name="offset" value="1269"/>
            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
            <output name="output" >
                <assert_contents>
                    <has_text text="#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count" />
                    <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Codon Variants
==============

Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
a synonymous or non-synonymous mutation.

    ]]></help>
    <citations>
		<citation type="bibtex">
			@misc{GitHubquasitoolscallcodonvar,
			title = {quasitools callcodonvar},
			publisher = {phac-nml},
			journal = {GitHub repository},
			url = {https://github.com/phac-nml/quasitools},
			}
		</citation>
    </citations>
</tool>