<tool id="callntvar" name="Nucleotide Variants" version="0.7.0">
    <description>Identifies nucleotide variants</description>
    <requirements>
          <requirement type="package" version="0.7.0">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

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

        #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="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" ftype="bam" />
            <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" />
            <output name="output" >
                <assert_contents>
                    <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
                    <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" />
                    <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" />
                    <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Nucleotide Variants
===================

Call nucleotide variants for a given BAM file and a supplied reference file.

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