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comparison vcfbedintersect.xml @ 0:8a482a9aa45d draft

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author devteam
date Thu, 19 Mar 2015 12:42:11 -0400
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1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3">
2 <description>Intersect VCF and BED datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio" />
8 <command>
9 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed":
10 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}"
11 #else:
12 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}"
13 #end if
14
15 </command>
16 <inputs>
17 <!-- selecting refernce source -->
18 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" />
19 <conditional name="bed_vs_interval">
20 <param name="bed_vs_interval_selector" type="select" label="BED dataset or an interval to intersect with">
21 <option value="bed">BED</option>
22 <option value="interval">Interval</option>
23 </param>
24 <when value="bed">
25 <param name="bed_input" type="data" format="bed" label="Select BED dataset" />
26 </when>
27 <when value="interval">
28 <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" />
29 </when>
30 </conditional>
31 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." />
32 </inputs>
33 <outputs>
34 <data format="vcf" name="out_file1" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="bed_vs_interval_selector" value="bed" />
39 <param name="bed_input" value="vcfannotate.bed" />
40 <param name="invert" value="False" />
41 <param name="vcf_input" value="vcflib.vcf"/>
42 <output name="out_file1" file="vcfbedintersect-test1.vcf"/>
43 </test>
44 <test>
45 <param name="bed_vs_interval_selector" value="interval" />
46 <param name="int_input" value="20:1-30000" />
47 <param name="invert" value="False" />
48 <param name="vcf_input" value="vcflib.vcf"/>
49 <output name="out_file1" file="vcfbedintersect-test2.vcf"/>
50 </test>
51 </tests>
52
53 <help>
54
55 Computes intersection between a VCF dataset and a set of genomic intervals defined as either a BED dataset (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) or a manually typed interval (in the form of chr:start-end).
56
57 ----
58
59 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
60 </help>
61 <expand macro="citations" />
62 </tool>