# HG changeset patch
# User ulfschaefer
# Date 1462360638 14400
# Node ID 10dca609454e1abab1e0d1ebc172ff7727fd4af2
# Parent  4e64e338cc06fac53e05bc4ccf791c257e558ca8
Uploaded

diff -r 4e64e338cc06 -r 10dca609454e filter_vcf.xml
--- a/filter_vcf.xml	Wed May 04 07:16:59 2016 -0400
+++ b/filter_vcf.xml	Wed May 04 07:17:18 2016 -0400
@@ -19,6 +19,11 @@
     filter_vcf.sh
 	$output
 	$input
+    #if str($onlygood) == "false":
+		onlygood
+	#else
+		NOTTHERE
+	#end if
 	#for $sf in $snp_filter:
 		#for $name, $param in $sf.snp_filter_type.iteritems():
 			#if $name not in [ "__current_case__", "snp_filter_type_selector" ]:
@@ -73,7 +78,10 @@
 			</when>
 		</conditional>
     </repeat>
-
+	<param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. ">
+			<option value="true" selected="true">Write all</option>
+			<option value="false">Write only good</option>
+    </param>
   </inputs>
 
   <outputs>