diff vcf_filter.xml @ 5:bdd1995c9e66

upgrade to mimodd version 0.1.6.1

--- a/vcf_filter.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/vcf_filter.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="vcf_filter" name="VCF Filter">
+<tool id="vcf_filter" name="VCF Filter" version="0.1.6.1">
   <description>Extracts lines from a vcf variant file based on field-specific filters</description>
   <macros>
     <import>toolshed_macros.xml</import>
@@ -28,6 +28,10 @@
 	#for $i in $datasets
 	    "$i.GQ"
 	#end for
+	--af
+	#for $i in $datasets
+	    "#echo ($i.AF or "::")#"
+	#end for
 	#end if
 	#if len($regions):
 	-r
@@ -54,6 +58,7 @@
 	<param name="GT" type="text" label="genotype pattern(s) for the inclusion of variants" help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." />
 	<param name="DP" type="integer" label="depth of coverage for the sample at the variant site" value = "0" help="keep only variants with at least this sample-specific coverage at the variant site" />
 	<param name="GQ" type="integer" label="genotype quality for the variant in the sample" value = "0" help="keep only variants for which the genotype prediction for the sample has at least this quality" />
+	<param name="AF" type="text" label="allelic fraction filter" help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" />
     </repeat>
     <repeat name="regions" title="Region Filter" default="0" min="0" help = "Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
       <param name="chrom" type="text" label="Chromosome" />