Mercurial > repos > ulfschaefer > phephenix

changeset 6:74f595df6e51 draft

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Uploaded
author ulfschaefer
date Thu, 16 Jun 2016 06:39:51 -0400
parents e2ee6acf8752
children 29a682a7dd16
files filter_vcf.xml
diffstat 1 files changed, 7 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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>