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+ | + | <macros> | +
| + | <macro name="reference_loc"> | +
| + | <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="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> | +
| + | <options from_data_table="mutect2_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> | +