--- a/variant_eval.xml	Mon Dec 02 10:36:02 2013 -0500
+++ b/variant_eval.xml	Sat Jan 18 07:21:33 2014 -0500
@@ -32,9 +32,9 @@
         #end if
     #end for
     
-    #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
+    #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}"
-        #if str( $dbsnp_rod_bind_type.dbsnp_known_names ):
+        #if $dbsnp_rod_bind_type.dbsnp_known_names
             -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
         #end if
     #end if
@@ -122,24 +122,25 @@
       </when>
     </conditional>
     
-    <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
+    <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">
       <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
-      <param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/>
-      <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/>
+      <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
+          <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+      </param>
+      <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/>
     </repeat>
-    
     <conditional name="dbsnp_rod_bind_type">
-      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
         <option value="set_dbsnp" selected="True">Set dbSNP</option>
         <option value="exclude_dbsnp">Don't set dbSNP</option>
       </param>
-      <when value="exclude_dbsnp">
-        <!-- Do nothing here -->
-      </when>
+      <when value="exclude_dbsnp" />
       <when value="set_dbsnp">
         <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
-        <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/>
-        <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
+        <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
+          <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+        </param>
+        <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
       </when>
     </conditional>
     
@@ -228,6 +229,7 @@
           <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
           <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
           <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_name" value="dbsnp" />
           <param name="dbsnp_known_names" value="True"/>
           <param name="comp_rod_bind" value="0" />
           <param name="gatk_param_type_selector" value="basic" />