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comparison vcf_filter.xml @ 5:bdd1995c9e66

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upgrade to mimodd version 0.1.6.1
author Wolfgang Maier
date Tue, 28 Jul 2015 23:21:11 +0200
parents ffee8534a5c4
children 85214e4428fd
comparison
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4:ffee8534a5c4 5:bdd1995c9e66
1 <tool id="vcf_filter" name="VCF Filter"> 1 <tool id="vcf_filter" name="VCF Filter" version="0.1.6.1">
2 <description>Extracts lines from a vcf variant file based on field-specific filters</description> 2 <description>Extracts lines from a vcf variant file based on field-specific filters</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
26 #end for 26 #end for
27 --gq 27 --gq
28 #for $i in $datasets 28 #for $i in $datasets
29 "$i.GQ" 29 "$i.GQ"
30 #end for 30 #end for
31 --af
32 #for $i in $datasets
33 "#echo ($i.AF or "::")#"
34 #end for
31 #end if 35 #end if
32 #if len($regions): 36 #if len($regions):
33 -r 37 -r
34 #for $i in $regions 38 #for $i in $regions
35 #if $i.stop: 39 #if $i.stop:
52 <repeat name="datasets" title="Sample-specific Filter" default="0" min="0"> 56 <repeat name="datasets" title="Sample-specific Filter" default="0" min="0">
53 <param name="sample" type="text" label="sample" help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." /> 57 <param name="sample" type="text" label="sample" help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." />
54 <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." /> 58 <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." />
55 <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" /> 59 <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" />
56 <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" /> 60 <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" />
61 <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" />
57 </repeat> 62 </repeat>
58 <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."> 63 <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.">
59 <param name="chrom" type="text" label="Chromosome" /> 64 <param name="chrom" type="text" label="Chromosome" />
60 <param name="start" type="text" label="Region Start" /> 65 <param name="start" type="text" label="Region Start" />
61 <param name="stop" type="text" label="Region End" /> 66 <param name="stop" type="text" label="Region End" />