# HG changeset patch
# User ulfschaefer
# Date 1466073591 14400
# Node ID 74f595df6e51133f5495d0746e8ec124f0c2c163
# Parent  e2ee6acf8752632ff53c5b78ad699ccd846ea318
Uploaded

diff -r e2ee6acf8752 -r 74f595df6e51 filter_vcf.xml
--- a/filter_vcf.xml	Thu Jun 16 06:39:37 2016 -0400
+++ b/filter_vcf.xml	Thu Jun 16 06:39:51 2016 -0400
@@ -19,6 +19,7 @@
     filter_vcf.sh
 	$output
 	$input
+    $ref_fa
     #if str($onlygood) == "false":
 		onlygood
 	#else
@@ -36,6 +37,8 @@
   <inputs>
     <param name="input" type="data" format="vcf" label="VCF File to filter" />
 
+    <param name="ref_fa" type="data" format="fasta" label="Reference genome fasta file" help="REQUIRED."/>
+
     <repeat name="snp_filter" title="SNP Filter" help="">
         <conditional name="snp_filter_type">
 			<param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
@@ -108,5 +111,9 @@
 
 \-\-output OUTPUT, -o OUTPUT	Location for filtered VCF to be written.
 
+\-\-reference REFERENCE, -r REFERENCE   mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF.
+
+\-\-only-good           Write only variants that PASS all filters (default all variants are written).
+
   </help>
 </tool>