<tool id="aavariants" name="Amino Acid Variants" version="0.5.1">
    <description>Identifies amino acid mutations</description>
    <requirements>
        <requirement type="package" version="0.5.1">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
		quasitools call aavar $input_bam $ref_file $input_genes 
		
		#if $var_file:
			$var_file 
		#end if

        #if $mutation_db:
        	$mutation_db
        #end if

		#if $min_freq:
			-f $min_freq 
		#end if

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

        -o output.vcf

    ]]></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="input_genes" type="data" format="bed" optional="false" label="Gene file" />
		<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." />
        <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
        <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." />
        <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/>
    </inputs>
    <outputs>
        <data format="vcf" name="output" from_work_dir="output.vcf" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="align.bam" />
            <param name="ref_file" value="hxb2_pol.fas" />
            <param name="var_file" value="nt_variants.vcf" />
            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
            <param name="min_freq" value="0.01" />
            <output name="output" >
                <assert_contents>
                    <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
                    <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." />
                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." />
                    <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." />
                    <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." />
                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." />
                    <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Amino Acid Variants
===================

Identifies amino acid mutations for a BAM file.



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