Mercurial > repos > wolma > mimodd
diff vcf_filter.xml @ 23:5db0545b9004 draft
update to v0.1.7.3
| author | wolma |
|---|---|
| date | Thu, 21 Jul 2016 03:55:49 -0400 |
| parents | c46406466625 |
| children |
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--- a/vcf_filter.xml Sun Jun 12 07:39:46 2016 -0400 +++ b/vcf_filter.xml Thu Jul 21 03:55:49 2016 -0400 @@ -1,9 +1,9 @@ -<tool id="vcf_filter" name="VCF Filter" version="0.1.7.2"> +<tool id="vcf_filter" name="VCF Filter" version="0.1.7.3"> <description>Extracts lines from a vcf variant file based on field-specific filters</description> <macros> <import>toolshed_macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements" /> <version_command>python3 -m MiModD version -q</version_command> <command> python3 -m MiModD vcf-filter @@ -52,29 +52,29 @@ </command> <inputs> - <param name="inputfile" type="data" format="vcf" label="VCF input file" /> - <repeat name="datasets" title="Sample-specific Filter" default="0" min="0"> - <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." /> - <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" /> + <param format="vcf" label="VCF input file" name="inputfile" type="data" /> + <repeat default="0" min="0" name="datasets" title="Sample-specific Filter"> + <param 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." label="sample" name="sample" type="text" /> + <param 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." label="genotype pattern(s) for the inclusion of variants" name="GT" type="text" /> + <param help="keep only variants with at least this sample-specific coverage at the variant site" label="depth of coverage for the sample at the variant site" name="DP" type="integer" value="0" /> + <param help="keep only variants for which the genotype prediction for the sample has at least this quality" label="genotype quality for the variant in the sample" name="GQ" type="integer" value="0" /> + <param 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" label="allelic fraction filter" name="AF" type="text" /> </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" /> - <param name="start" type="text" label="Region Start" /> - <param name="stop" type="text" label="Region End" /> + <repeat default="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." min="0" name="regions" title="Region Filter"> + <param label="Chromosome" name="chrom" type="text" /> + <param label="Region Start" name="start" type="text" /> + <param label="Region End" name="stop" type="text" /> </repeat> - <param name="vartype" type="select" label="Select the types of variants to include in the output"> + <param label="Select the types of variants to include in the output" name="vartype" type="select"> <option value="">all types of variants</option> <option value="--no-indels">exclude indels</option> <option value="--indels-only">only indels</option> </param> - <param name="vfilter" type="text" label="sample" help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." /> + <param help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." label="sample" name="vfilter" type="text" /> </inputs> <outputs> - <data name="outputfile" format="vcf" /> + <data format="vcf" name="outputfile" /> </outputs> <help> @@ -105,21 +105,21 @@ *Simple genotype pattern* -genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant +genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant *Complex genotype pattern* -genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype +genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype *Multiple sample-specific filters* Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1: -==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant +==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant *Combining sample-specific filter criteria* genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9 -==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9 +==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9 **and** at least three reads from the sample cover the variant site **TIP:** @@ -130,4 +130,4 @@ </help> -</tool> +</tool> \ No newline at end of file