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comparison vcffilter.xml @ 3:0e7ec249e679 draft default tip

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author anton
date Mon, 15 Sep 2014 14:51:08 -0400
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2:a1c14d64b003 3:0e7ec249e679
1 <tool id="vcffilter" name="VCFfilter:" version="0.0.2"> 1 <tool id="vcffilter2" name="VCFfilter:" version="0.0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="86723982aa">vcflib</requirement> 3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
4 </requirements> 4 </requirements>
5 <description>filter VCF data in a variety of attributes</description> 5 <description>filter VCF data in a variety of attributes</description>
6 <command> 6 <command>
7 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> 7 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
8 ln -s "${input1}" input1.vcf.gz &amp;&amp; 8 ln -s "${input1}" input1.vcf.gz &amp;&amp;
19 <mapping initial="none"> 19 <mapping initial="none">
20 <add source="&apos;" target="__sq__"/> 20 <add source="&apos;" target="__sq__"/>
21 </mapping> 21 </mapping>
22 </sanitizer> 22 </sanitizer>
23 </param> 23 </param>
24 <param format="vcf_bgzip" name="input1" type="data" label="From"> 24 <param format="vcf_bgzip" name="input1" type="data" label="VCF dataset to filter">
25 <conversion name="Tabixized_input" type="tabix" /> 25 <conversion name="Tabixized_input" type="tabix" />
26 </param> 26 </param>
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data format="vcf" name="out_file1" /> 29 <data format="vcf" name="out_file1" />
35 <output name="out_file1" file="vcffilter-test1.vcf"/> 35 <output name="out_file1" file="vcffilter-test1.vcf"/>
36 </test> 36 </test>
37 </tests> 37 </tests>
38 <help> 38 <help>
39 39
40 You can specify the following option the **Specify filtering expression** box in any combination:: 40 You can specify the following options within the **Specify filtering expression** box in any combination::
41 41
42 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter 42 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
43 -g, --genotype-filter specifies a filter to apply to the genotype fields of records 43 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
44 -s, --filter-sites filter entire records, not just alleles 44 -s, --filter-sites filter entire records, not just alleles
45 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records 45 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
46 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records 46 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
47 -A, --append-filter append the existing filter tag, don't just replace it 47 -A, --append-filter append the existing filter tag, don't just replace it
48 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag 48 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
49 -v, --invert inverts the filter, e.g. grep -v 49 -v, --invert inverts the filter, e.g. grep -v
50 -o, --or use logical OR instead of AND to combine filters 50 -o, --or use logical OR instead of AND to combine filters
51 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g 51 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
52 52
53 Filters are specified in the form {ID} {operator} {value}:: 53 Filters are specified in the form {ID} {operator} {value}::
54 54
55 -f "DP > 10" # for info fields 55 -f "DP > 10" # for info fields
56 -g "GT = 1|1" # for genotype fields 56 -g "GT = 1|1" # for genotype fields
57 -f "CpG" # for 'flag' fields 57 -f "CpG" # for 'flag' fields
58 58
59 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. 59 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.
60 60
61 Operators can be any of: =, !, &lt;, &gt;, pipe, &amp; 61 Operators can be any of: =, !, &lt;, &gt;, pipe, &amp;
62 62
63 63
64 To restrict output to a specific location use -r option (much be used in conjunction with -g or -f):: 64 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
65 65
66 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 66 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
67 -r chrX # only output call on chromosome X 67 -r chrX # only output call on chromosome X
68 68
69 ----- 69 -----