<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.7.1">r-optparse</requirement>
            <requirement type="package" version="1.14.2">r-data.table</requirement>
            <requirement type="package" version="1.54.0">bioconductor-rtracklayer</requirement>
        </requirements>
    </xml>
    <xml name="fasta">
        <conditional name="fasta_file">
            <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA. The FASTA must be the same genome version as the GTF.">
                <option value="indexed" selected="true">Use a built-in FASTA </option>
                <option value="history">Use a FASTA from history</option>
            </param>
            <when value="indexed">
                <param name="fasta_pre_installed" type="select" help="Select the FASTA file from a list of pre-installed genomes" label="Select a FASTA file">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2" />
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="fasta_history" type="data" format="fasta" label="Select a FASTA file that matches the supplied GTF file" />
            </when>
        </conditional>
    </xml>
</macros>