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comparison vcfannotate.xml @ 3:28459b837ef8 draft default tip

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author anton
date Mon, 15 Sep 2014 14:48:28 -0400
parents 98961914308d
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2:98961914308d 3:28459b837ef8
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