--- a/macros.xml	Wed Jun 21 07:24:36 2017 -0400
+++ b/macros.xml	Wed Jun 21 09:38:09 2017 -0400
@@ -26,4 +26,24 @@
         <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>