<macros>
    <xml name="tag_options">
        <option value="A">A</option>
        <option value="B">B</option>
        <option value="C">C</option>
        <option value="D">D</option>
        <option value="E">E</option>
        <option value="F">F</option>
        <option value="G">G</option>
        <option value="H">H</option>
        <option value="I">I</option>
        <option value="J">J</option>
        <option value="K">K</option>
        <option value="L">L</option>
        <option value="M">M</option>
        <option value="N">N</option>
        <option value="O">O</option>
        <option value="P">P</option>
        <option value="Q">Q</option>
        <option value="R">R</option>
        <option value="S">S</option>
        <option value="T">T</option>
        <option value="U">U</option>
        <option value="V">V</option>
        <option value="W">W</option>
        <option value="X">X</option>
        <option value="Y">Y</option>
    </xml>
    <xml name="reference_source_conditional" token_reference_type="reference_type">
        <conditional name="@REFERENCE_TYPE@_source">
            <param name="reference_source_selector" type="select" label="Will you select a @REFERENCE_TYPE@ 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 @REFERENCE_TYPE@ genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using @REFERENCE_TYPE@ reference genome" help="Select @REFERENCE_TYPE@ genome from the list" optional="True">
                    <options from_data_table="bwa_mem_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" optional="True"/>
            </when>
        </conditional>
    </xml>
</macros>