<macros>
    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>

    <token name="@set_fasta_index@"><![CDATA[
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s '${reference_source.ref_file}' reference.fa &&
        samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
    #else:
        ln -s '${source.index.fields.path}' reference.fa &&
        ln -s '${source.index.fields.path}.fai' reference.fa.fai &&
    #end if
    ]]></token>

    <macro name="reference_source_conditional">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="cached">Use a built-in genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="index" type="select" label="Using built-in genome" help="Select genome from the list">
                    <options from_data_table="fasta_indexes">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No indexes are available" />
                    </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="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
                    help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
    </macro>
</macros>