<macros>
    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
    <token name="@TOOL_VERSION@">0.6.2</token>
    <token name="@VERSION_SUFFIX@">8</token>
    <token name="@PROFILE@">23.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.6.2">snp-pileup</requirement>
            <requirement type="package" version="1.22">bcftools</requirement>
            <requirement type="package" version="1.22.1">samtools</requirement>
            <requirement type="package" version="1.22.1">htslib</requirement>
            <requirement type="package" version="20250822">parallel</requirement>
            <requirement type="package" version="9.5">coreutils</requirement>
            <requirement type="package" version="0.6.2">r-facets</requirement>
            <requirement type="package" version="2.2.5">r-argparse</requirement>

        </requirements>
    </xml>    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @article{shen2016facets,
                  title={FACETS: allele-specific copy number and clonal heterogeneity analysis tool for cancer sequencing data},
                  author={Shen, Ronglai and Seshan, Venkatraman E},
                  journal={Nucleic acids research},
                  volume={44},
                  number={12},
                  pages={e131--e131},
                  year={2016},
                  publisher={Oxford University Press}
                }
            </citation>
            </citations>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" level="fatal" description="Error during script execution." />
        </stdio>
    </xml>

</macros>