Mercurial > repos > anton > vcfannotate
comparison vcfannotate.xml @ 3:28459b837ef8 draft default tip
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author | anton |
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date | Mon, 15 Sep 2014 14:48:28 -0400 |
parents | 98961914308d |
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2:98961914308d | 3:28459b837ef8 |
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1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.2"> | 1 <tool id="vcfannotate" name="VCFannotate:" 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>Intersect VCF records with BED annotations</description> | 5 <description>Intersect VCF records with BED annotations</description> |
6 <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> | 6 <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command> |
7 <inputs> | 7 <inputs> |
8 <param format="vcf" name="input" type="data" label="Select VCF dataset"/> | 8 <param format="vcf" name="input" type="data" label="Select VCF dataset"/> |
9 <param name="bed_data" type="data" format="bed" label="BED datasets to itersect with"/> | 9 <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/> |
10 <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"/> | 10 <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"/> |
11 </inputs> | 11 </inputs> |
12 <outputs> | 12 <outputs> |
13 <data format="vcf" name="out_file1" /> | 13 <data format="vcf" name="out_file1" /> |
14 </outputs> | 14 </outputs> |
20 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> | 20 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" /> |
21 </test> | 21 </test> |
22 </tests> | 22 </tests> |
23 <help> | 23 <help> |
24 | 24 |
25 Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference sequences in the VCF file. | 25 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. |
26 | 26 |
27 ----- | 27 ----- |
28 | 28 |
29 .. class:: infomark | 29 .. class:: infomark |
30 | 30 |