Mercurial > repos > wolma > mimodd_main
diff vcf_filter.xml @ 0:f0f2795de2c7 draft
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
| author | wolma |
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| date | Tue, 19 Dec 2017 04:54:04 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf_filter.xml Tue Dec 19 04:54:04 2017 -0500 @@ -0,0 +1,205 @@ +<tool id="mimodd_vcf_filter" name="MiModD VCF Filter" version="@MIMODD_WRAPPER_VERSION@"> + <description> + extracts lines from a vcf variant file based on field-specific filters + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mimodd vcf-filter + '$inputfile' -o '$outputfile' + #if len($datasets): + -s + #for $i in $datasets + '$i.sample' + #end for + --gt + #for $i in $datasets + ## remove whitespace from free-text input + '#echo ("".join($i.GT.split()) or "ANY")#' + #echo " " + #end for + --dp + #for $i in $datasets + $i.DP + #end for + --gq + #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 + #for $i in $regions + #if $i.stop: + '$i.chrom:$i.start-$i.stop' + #else: + '$i.chrom:$i.start' + #end if + #end for + #end if + #if $vfilter: + --vfilter + ## remove ',' and replace with ' ' + '#echo ('" "'.join($vfilter.split(',')))#' + #end if + $vartype + ]]></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."> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in sample names." /> + </param> + <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."> + <validator type="expression" message="Malformed genotype pattern">not value or all(c.isdigit() or c in './|' for token in value.split(',') for c in token.strip(' '))</validator> + </param> + <param name="DP" type="integer" value="0" + label="depth of coverage for the sample at the variant site" + help="keep only variants with at least this sample-specific coverage at the variant site" /> + <param name="GQ" type="integer" value="0" + label="genotype quality for the variant in the sample" + 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"> + <validator type="expression" message="Malformed allelic fraction filter">not value or all(c.isdigit() or c in '.:' for c in value)</validator> + </param> + </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"> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in chromosome names." /> + </param> + <param name="start" type="text" label="Region Start"> + <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> + </param> + <param name="stop" type="text" label="Region End"> + <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> + </param> + </repeat> + <param name="vartype" type="select" + label="Select the types of variants to include in the output"> + <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."> + <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in sample names." /> + </param> + </inputs> + + <outputs> + <data name="outputfile" format="vcf" /> + </outputs> + + <tests> + <test> + <param name="inputfile" value="a.vcf" /> + <repeat name="datasets"> + <param name="sample" value="N2" /> + <param name="GT" value="0/0" /> + </repeat> + <output name="outputfile" ftype="vcf" compare="diff"> + <assert_contents> + <has_text text="GT:PL:DP:DPR:GQ	0/0" /> + <not_has_text text="GT:PL:DP:DPR:GQ	1/1" /> + <not_has_text text="GT:PL:DP:DPR:GQ	0/1" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputfile" value="a.vcf" /> + <repeat name="regions"> + <param name="chrom" value="chrX" /> + </repeat> + <output name="outputfile" ftype="vcf"> + <assert_contents> + <has_text text="chrX	" /> + <not_has_text text="chrI	" /> + <not_has_text text="chrII	" /> + <not_has_text text="chrIII	" /> + <not_has_text text="chrIV	" /> + <not_has_text text="chrV	" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputfile" value="a.vcf" /> + <param name="vartype" value="--no-indels" /> + <param name="vfilter" value="ot266" /> + <output name="outputfile" ftype="vcf"> + <assert_contents> + <not_has_text text="INDEL;" /> + <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ot266" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +.. class:: infomark + + **What it does** + +The tool filters a variant file in VCF format to generate a new VCF file with only a subset of the original variants. + +The following types of variant filters can be set up: + +1) Sample-specific filters: + + Filter variants based on their characteristics in the sequenced reads of a specific sample. Multiple sample-specific filters are combined by logical AND, i.e., only variants that pass ALL sample-specific filters are kept. + +2) Region filters: + + Filter variants based on the genomic region they affect. Multiple region filters are combined by logical OR, i.e., variants passing ANY region filter are kept. + +3) Variant type filter: + + Filter variants by their type, i.e. whether they are single nucleotide variations (SNVs) or indels + +In addition, the *sample* filter can be used to reduce the samples encoded in a multi-sample VCF file to just those specified by the filter. +The *sample* filter is included mainly for compatibility reasons: if an external tool cannot deal with the multisample file format, but instead looks only at the first sample-specific column of the file, you can use the filter to turn the multi-sample file into a single-sample file. Besides, the filter can also be used to change the order of the samples since it will sort the samples in the order specified in the filter field. + +**Examples of sample-specific filters:** + +*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 + +*Complex genotype pattern* + +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 + +*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 +**and** at least three reads from the sample cover the variant site + +**TIP:** + +As in the example above, genotype quality is typically most useful in combination with a genotype pattern. +It acts then, effectively, to make the genotype filter more stringent. + +@HELP_FOOTER@ + ]]></help> + <expand macro="citations" /> +</tool>