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1 <macros>
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2 <macro name="reference_loc">
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3 <conditional name="reference_source">
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4 <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">
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5 <option value="cached">Use a built-in genome index</option>
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6 <option value="history">Use a genome from history and build index</option>
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7 </param>
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8 <when value="cached">
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9 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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10 <options from_data_table="covacs_gatk_indexes">
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11 <filter type="sort_by" column="2" />
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12 <validator type="no_options" message="No indexes are available" />
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13 </options>
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14 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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15 </param>
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16 </when>
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17 <when value="history">
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18 <param name="ref_file_h" 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" />
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19 </when>
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20 </conditional>
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21 </macro>
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22 </macros>
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