--- a/gatk2_macros.xml	Mon Dec 02 10:36:02 2013 -0500
+++ b/gatk2_macros.xml	Sat Jan 18 07:21:33 2014 -0500
@@ -1,17 +1,23 @@
 <macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.1.19">samtools</requirement>
-            <requirement type="set_environment">GATK2_PATH</requirement>
-            <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
-        </requirements>
-    </xml>
-    <token name="@THREADS@">
-        --num_threads \${GALAXY_SLOTS:-4}
-    </token>
-    <token name="@JAR_PATH@">
-        java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
-    </token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package">gatk2</requirement>
+      <requirement type="package" version="0.1.19">samtools</requirement>
+      <requirement type="set_environment">GATK2_PATH</requirement>
+      <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
+    </requirements>
+  </xml>
+  <token name="@THREADS@">
+    --num_threads \${GALAXY_SLOTS:-4}
+  </token>
+  <token name="@JAR_PATH@">
+    java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
+  </token>
+  <token name="@DBSNP_OPTIONS@">
+    #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
+        -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
+    #end if
+  </token>
   <template name="standard_gatk_options">
     ##start standard gatk options
     #if $gatk_param_type.gatk_param_type_selector == "advanced":
@@ -311,6 +317,21 @@
       <option value="history">History</option>
     </param>
   </xml>
+  <xml name="dbsnp_param">
+    <conditional name="dbsnp_rod_bind_type">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
+        <option value="set_dbsnp" selected="True">Set dbSNP</option>
+        <option value="exclude_dbsnp">Don't set dbSNP</option>
+      </param>
+      <when value="exclude_dbsnp" />
+      <when value="set_dbsnp">
+        <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
+        <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
+          <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+        </param>
+      </when>
+    </conditional>
+  </xml>
   <token name="@CITATION_SECTION@">------
 
 **Citation**