<macros>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@TOOL_VERSION@">1.8.3</token>
    <xml name="ref_select">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file">
                <option value="cached" selected="true">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Reference Genome File">
                    <options from_data_table="fasta_indexes"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" format="fasta" type="data" label="Reference Genome File" />
            </when>
        </conditional>
    </xml>
    <xml name="stdio">
        <stdio>
            <regex match="java.lang.OutOfMemoryError" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
        </stdio>
    </xml>
    <xml name="input_default">
        <param name="tumor" type="data" format="bam" label="Tumor file" />
        <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
    </xml>
</macros>