Mercurial > repos > devteam > vcffilter
comparison vcffilter.xml @ 0:34c3b846e0b6 draft
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| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 14:27:51 -0400 |
| parents | |
| children | e729e584cd6f |
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| -1:000000000000 | 0:34c3b846e0b6 |
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| 1 <tool id="vcffilter2" name="VCFfilter:" version="0.0.3"> | |
| 2 <description>filter VCF data in a variety of attributes</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 7 <requirement type="package" version="0.2.6">tabix</requirement> | |
| 8 </expand> | |
| 9 <expand macro="stdio" /> | |
| 10 <command> | |
| 11 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> | |
| 12 ln -s "${input1}" input1.vcf && | |
| 13 bgzip input1.vcf && | |
| 14 tabix -p vcf input1.vcf.gz && | |
| 15 vcffilter ${filterList} input1.vcf.gz > "${out_file1}" | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="filterList" size="40" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> | |
| 20 <sanitizer> | |
| 21 <valid initial="string.printable"> | |
| 22 <remove value="'"/> | |
| 23 </valid> | |
| 24 <mapping initial="none"> | |
| 25 <add source="'" target="__sq__"/> | |
| 26 </mapping> | |
| 27 </sanitizer> | |
| 28 </param> | |
| 29 <param format="vcf" name="input1" type="data" label="VCF dataset to filter"> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="vcf" name="out_file1" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="filterList" value="-f "DP > 10""/> | |
| 38 <param name="input1" value="vcflib.vcf"/> | |
| 39 <output name="out_file1" file="vcffilter-test1.vcf"/> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 43 | |
| 44 You can specify the following options within the **Specify filtering expression** box in any combination:: | |
| 45 | |
| 46 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter | |
| 47 -g, --genotype-filter specifies a filter to apply to the genotype fields of records | |
| 48 -s, --filter-sites filter entire records, not just alleles | |
| 49 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records | |
| 50 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records | |
| 51 -A, --append-filter append the existing filter tag, don't just replace it | |
| 52 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag | |
| 53 -v, --invert inverts the filter, e.g. grep -v | |
| 54 -o, --or use logical OR instead of AND to combine filters | |
| 55 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) | |
| 56 | |
| 57 Filters are specified in the form {ID} {operator} {value}:: | |
| 58 | |
| 59 -f "DP > 10" # for info fields | |
| 60 -g "GT = 1|1" # for genotype fields | |
| 61 -f "CpG" # for 'flag' fields | |
| 62 | |
| 63 Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. | |
| 64 | |
| 65 Operators can be any of: =, !, <, >, pipe, & | |
| 66 | |
| 67 | |
| 68 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: | |
| 69 | |
| 70 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 | |
| 71 -r chrX # only output call on chromosome X | |
| 72 | |
| 73 ----- | |
| 74 | |
| 75 Vcffilter @IS_PART_OF_VCFLIB@ | |
| 76 </help> | |
| 77 <expand macro="citations" /> | |
| 78 </tool> |