--- a/macros.xml	Tue Jul 10 13:36:24 2018 -0400
+++ b/macros.xml	Sun Jul 15 09:19:48 2018 -0400
@@ -23,6 +23,35 @@
         </citations>
     </xml>
 
+    <xml name="input_pileups">
+        <conditional name="pileup">
+           <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
+               <option value="separated">As separated normal and tumor files</option>
+               <option value="combined">Normal and Tumor combined in one file</option>
+           </param>
+           <when value="separated">
+                <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
+                <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
+           </when>
+           <when value="combined">
+                <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
+           </when>
+        </conditional>
+    </xml>
+
+    <token name="@INPUT_PILEUPS@">
+        #if $pileup.pileup_select == 'separated'
+           '${pileup.normal_pileup}'
+           '${pileup.tumor_pileup}'
+           galaxy_out
+        #else:
+           '${pileup.combined_pileup}'
+            galaxy_out
+           --mpileup 1
+        #end if
+        
+    </token>
+
     <xml name="min_coverage">
         <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
             label="Minimum read depth" help="Minimum depth at a position to make a call"/>