<tool id="aacoverage" name="Amino Acid Coverage" version="0.4.2">
    <description>Builds an aa census and returns its coverage</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 aacoverage $input_bam $ref_file $input_genes -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="input_genes" type="data" format="bed" optional="false" label="Gene 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="input_genes" ftype="bed" value="hxb2_pol.bed" />
            <output name="output" >
                <assert_contents>
                    <has_text text="frame: 0" />
                    <has_text text="1,0" />
                    <has_text text="948,1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Amino Acid Coverage
===================

Builds an amino acid census and returns its coverage.

**Output**

A file with one entry per line with the AA position and the coverage at the position.

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