<macros>
    <token name="@TOOL_VERSION@">1.3.5</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement>
            <requirement type="package" version="1.12">samtools</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{1207.3907,
                    Author = {Erik Garrison},
                    Title = {Haplotype-based variant detection from short-read sequencing},
                    Year = {2012},
                    Eprint = {arXiv:1207.3907},
                    url = {http://arxiv.org/abs/1207.3907}
                }
            </citation>
            <yield />
        </citations>
    </xml>
    <xml name="validation">
        <validator type="unspecified_build" />
        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
    </xml>
    <xml name="input_bam">
        <conditional name="batchmode">
            <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio">
                <option value="individual" selected="true">Run individually</option>
                <option value="merge">Merge output VCFs</option>
            </param>
            <when value="individual">
                <param name="input_bams" type="data" format="bam,cram" label="BAM or CRAM dataset">
                    <yield />
                </param>
            </when>
            <when value="merge">
                <param name="input_bams" type="data" format="bam,cram" multiple="true" label="BAM or CRAM dataset(s)">
                    <yield />
                </param>
            </when>
        </conditional>
    </xml>
    <token name="@COVERAGE@">
        --min-coverage ${coverage_options.min_coverage}
        --skip-coverage ${coverage_options.skip_coverage}
        --limit-coverage ${coverage_options.limit_coverage}
    </token>
    <xml name="par_min_cov">
        <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
        <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
        <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
    </xml>
</macros>