Mercurial > repos > ulfschaefer > phephenix

changeset 17:10dca609454e draft

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Uploaded
author ulfschaefer
date Wed, 04 May 2016 07:17:18 -0400
parents 4e64e338cc06
children ec61f77332ff
files filter_vcf.xml
diffstat 1 files changed, 9 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>