--- a/TV-vs-background.xml	Mon Aug 03 05:03:16 2015 -0400
+++ b/TV-vs-background.xml	Mon Aug 03 05:45:16 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="t-vs-vnormal" name="Virtual Normal Correction SmallVars" version="1.6">
+<tool id="t-vs-vnormal" name="Virtual Normal Correction SmallVars" version="1.7">
 	<description> Filter small variants based on presence in Virtual Normal set  </description>
 
 	<requirements>		
@@ -9,15 +9,11 @@
 	TV-vs-background.sh 
 		--variants $variants
 		--reference ${reference.fields.reference_crr_cgatools}
-		#if $virtnorm.VNset == "diversity":
-			--VN_varfiles ${reference.fields.VN_genomes_varfiles_list} 
-		#else
-			--VN_varfiles ${reference.fields.VN_genomes_varfiles_list_1000G} 
-		#end if
+		--VN_varfiles "${reference.fields.VN_genomes_varfiles_list}${VNset}"
 		--threshold $threshold
-                --thresholdhc $thresholdhc
+		--thresholdhc $thresholdhc
 		--outputfile_all $output_all
-		--outputfile_filtered $output_filtered		
+		--outputfile_filtered $output_filtered
 	</command>
 	
 	<inputs>
@@ -25,34 +21,26 @@
 		<!--select build-->
 		<param name="reference" type="select" label="Select Build">
 			<options from_data_table="virtual_normal_correction" />
-			<filter type="data_meta" ref="variants" key="dbkey" column="0" />
 		</param>
-		<conditional name="virtnorm" >
+		
+		<!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
 		<param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples, for hg18 54 genomes will be used.">
-			<option value="diversity" > CG Diversity Panel and trios (54 Genomes) </option>
-			<option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
-		</param> 
-		</conditional>
-				
-		<param name="threshold" type="text" value="1" label="Threshold: Filter variants if present in at least this number of the background genomes"/>
-                <param name="thresholdhc" type="text" value="10" label="High Confidence Threshold: Label a somatic variant as high-confidence if locus was fully called in at least this many normal genomes" help="Please adjust according to number of normals used and desired stringency. "/>
+			<option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option>
+			<option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
+			<option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
+                        <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
+		</param>
+					
+		<param name="threshold" type="text" value="1" label="Filter out variants present in at least this number of the virtual normal genomes"/>
+        <param name="thresholdhc" type="text" value="10" label="High Confidence Threshold: Label a somatic variant as high-confidence if locus was fully called in at least this many normal genomes" help="Please adjust according to number of normals used and desired stringency. "/>
 		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional. For example sample name."/>
-		<!--<param name="debug" type="select" label="individual level annotations?" help="get a columns per normal sample whether variant was present (only available for fully public normal samples)">
-			<option value="N" > No  </option>
-			<option value="Y" > Yes </option>
-		</param>
-                -->
 	</inputs>
 
   <outputs>
-    <data format="tabular" name="output_all" label="${fname} All variants for ${tool.name} on ${on_string}"/>		
-    <data format="tabular" name="output_filtered" label="${fname} Filtered variants for ${tool.name} on  ${on_string}"/>
-    <data format="tabular" name="output_filtered_highconf" label="${fname} High Confidence Filtered variants for ${tool.name} on  ${on_string}" from_work_dir="output_filtered_highconf.tsv"/>
-    <!--<data format="tabular" name="output_filtered" label="${fname} Filtered variants for ${tool.name} on  ${on_string}"/>
-	<data format="tabular" name="output_expanded" from_work_dir="output_expanded" label="${fname} expanded annotation for ${tool.name} on  ${on_string}">
-		<filter> $debug == "Y" </filter>
-	</data>	
-    -->
+    <data format="tabular" name="output_all" label="All variants for ${tool.name} on ${on_string}"/>		
+    <data format="tabular" name="output_filtered" label="Filtered variants for ${tool.name} on  ${on_string}"/>	
+	<data format="tabular" name="output_filtered_highconf" label="${fname} High Confidence Filtered variants for ${tool.name} on  ${on_string}" from_work_dir="output_filtered_highconf.tsv"/>
+
   </outputs>
 
 	<help>