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comparison vcfannotate.xml @ 0:87d916fbb7c4 draft

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author devteam
date Thu, 19 Mar 2015 12:39:51 -0400
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1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.3">
2 <description>Intersect VCF records with BED annotations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio" />
8 <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
9 <inputs>
10 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
11 <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
12 <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
13 </inputs>
14 <outputs>
15 <data format="vcf" name="out_file1" />
16 </outputs>
17 <tests>
18 <test>
19 <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
20 <param name="key_option" value="BED-features"/>
21 <param name="input" value="vcflib.vcf"/>
22 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
23 </test>
24 </tests>
25 <help>
26
27 Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file.
28
29 -----
30
31 .. class:: infomark
32
33
34 **Example**:
35
36 The following VCF line::
37
38 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
39 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
40
41 will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
42
43 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
44 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
45
46 ----
47
48 Vcfannotate @IS_PART_OF_VCFLIB@
49 </help>
50 <expand macro="citations" />
51 </tool>