<tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Identifies amino acid mutations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[

        ln -s $input_bam '${input_bam.name}' &&
        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&

		quasitools call aavar '${input_bam.name}' $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"/>
                    <has_text_matching expression="0.0779" />
                    <has_text_matching expression="0.0103;CAT=.;SRVL=." />
                    <has_text_matching expression="0.0163;CAT=.;SRVL=." />
                    <has_text_matching expression="0.0148;CAT=.;SRVL=." />
                    <has_text_matching expression="0.0234;CAT=.;SRVL=." />
                    <has_text_matching expression="0.0159;CAT=.;SRVL=." />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

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

Identifies amino acid mutations for a BAM file.



    ]]></help>
    <expand macro="citations" />
</tool>