Mercurial > repos > devteam > vcfannotate
annotate vcfannotate.xml @ 1:829d46588cf5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:57:42 -0500 |
| parents | 87d916fbb7c4 |
| children | d64204113938 |
| rev | line source |
|---|---|
| 0 | 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"/> | |
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829d46588cf5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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12 <param name="key_option" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/> |
| 0 | 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> |