Mercurial > repos > anton > vcffilter
diff vcffilter.xml @ 0:f84ad3b2d320
Imported from capsule None
author | anton |
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date | Wed, 11 Jun 2014 17:11:22 -0400 |
parents | |
children | fd10ad2f8f22 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcffilter.xml Wed Jun 11 17:11:22 2014 -0400 @@ -0,0 +1,74 @@ +<tool id="vcffilter" name="VCFfilter:" version="0.0.1"> +<requirements> + <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> +</requirements> + <description>filter VCF data in a variety of attributes</description> + <command> + <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> + ln -s "${input1}" input1.vcf.gz && + ln -s "${Tabixized_input}" input1.vcf.gz.tbi && + vcffilter ${filterList} input1.vcf.gz > "${out_file1}" + </command> + + <inputs> + <param name="filterList" size="40" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param format="vcf_bgzip" name="input1" type="data" label="From"> + <conversion name="Tabixized_input" type="tabix" /> + </param> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="filterList" value="-f "DP > 10""/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcffilter-test1.vcf"/> + </test> +</tests> + <help> + +You can specify the following option the **Specify filtering expression** box in any combination:: + + -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter + -g, --genotype-filter specifies a filter to apply to the genotype fields of records + -s, --filter-sites filter entire records, not just alleles + -t, --tag-pass tag vcf records as positively filtered with this tag, print all records + -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records + -A, --append-filter append the existing filter tag, don't just replace it + -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag + -v, --invert inverts the filter, e.g. grep -v + -o, --or use logical OR instead of AND to combine filters + -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g + +Filters are specified in the form {ID} {operator} {value}:: + + -f "DP > 10" # for info fields + -g "GT = 1|1" # for genotype fields + -f "CpG" # for 'flag' fields + +Any number of filters may be specified. They are combined via logical AND unless --or is specified on the command line. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. + +Operators can be any of: =, !, <, >, pipe, & + + +To restrict output to a specific location use -r option (much be used in conjunction with -g or -f):: + + -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 + -r chrX # only output call on chromosome X + +----- + +Vcffilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + +</help> +</tool>