<tool id="drmutations" name="Drug Resistance Mutations" version="0.5.1">
    <description></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 drmutations $input_bam $ref_file $var_file $input_genes

        #if $mutation_db:
          $mutation_db
        #end if

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

        #if $reporting_thres:
            -t $reporting_thres
        #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="var_file" type="data" format="vcf" optional="false" label="Variants file" />
        <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
        <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" />
        <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="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1"
            help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/>
    </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="var_file" value="nt_variants.vcf" />
            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
            <param name="mutation_db" value="mutation_db.tsv" />
            <output name="output" >
                <assert_contents>
                    <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
                    <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Drug Resistance Mutations
=========================

Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).

------
Inputs
------

1. A BAM file.
2. A reference FASTA file.
3. A variants (.vcf) file.
4. A genes (.bed) file.
5. A mutation database (.tsv) file.

----------
Parameters
----------
1. The minimum required frequency for a variant to be considered. Defaults to 0.01.
2. The reporting threshold a mutation must pass to be included in the report.

-------
Outputs
-------

A CSV file containing the drug resistant mutations found.

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