--- a/JunctionDiff-vs-background.xml	Mon Aug 03 05:03:16 2015 -0400
+++ b/JunctionDiff-vs-background.xml	Mon Aug 03 05:45:16 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.6">
+<tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.8">
 	<description> Filter SVs based on presence in VN set </description>
 	
 	<requirements>		
@@ -9,32 +9,31 @@
 	JunctionDiff-vs-background.sh 
 		--variants $variants 
 		--reference ${reference.fields.reference_crr_cgatools} 
-		#if $virtnorm.VNset == "diversity"
-			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list} 
-		#else
-			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list_1000G} 
-		#end if
+		--VN_junctions ${reference.fields.VN_genomes_junctionfile_list}${VNset}
 		--cgatools_binary cgatools
 		--outputfile_filtered $output_filtered 
 		--scoreThresholdA $scoreThresholdA 
 		--scoreThresholdB $scoreThresholdB 
 		--distance $distance 
-		--minlength $minlength					
+		--minlength $minlength			
 	</command>
 	
 	<inputs>
+		<param name="variants" type="data" format="tabular" label="CG Junctions file"/>	
+		
 		<!--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" >
-		<param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples">
-			<option value="diversity" selected="true"> CG Diversity Panel and trios (54 Genomes) (hg18/hg19) </option>
-			<option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
+
+		<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="46_diversity.txt" > CG Diversity Panel (46 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>
-		</conditional>
-		<param name="variants" type="data" format="tabular" label="CG Junctions file"/>
+		
+			
 		<param name="scoreThresholdA" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from input genome"/>
 		<param name="scoreThresholdB" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from background genomes"/>
 		<param name="distance" type="text" value="200" label="Maximum distance between coordinates of potentially compatible junctions."/>		
@@ -48,9 +47,9 @@
 
   <outputs>
        <data format="tabular" name="output_filtered" label="${fname} Filtered junctions for ${tool.name} on  ${on_string}"/>		
-       <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on  ${on_string}">
-       	<filter> report == "Y" </filter>
-       </data>			  
+	   <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on  ${on_string}">
+		   <filter> report == "Y" </filter>
+	   </data>	
   </outputs>
 
 	<help>