Mercurial > repos > anton > vcfbedintersect
comparison vcfbedintersect.xml @ 0:7e8a201b4c1c
Imported from capsule None
| author | anton |
|---|---|
| date | Wed, 11 Jun 2014 17:11:32 -0400 |
| parents | |
| children | a83d472202c8 |
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| -1:000000000000 | 0:7e8a201b4c1c |
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| 1 <tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.1"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> | |
| 4 <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> | |
| 5 </requirements> | |
| 6 <description>Intersect VCF and BED datasets</description> | |
| 7 <command> | |
| 8 #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": | |
| 9 vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" | |
| 10 #else: | |
| 11 vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" | |
| 12 #end if | |
| 13 | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <!-- selecting refernce source --> | |
| 17 <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> | |
| 18 <conditional name="bed_vs_interval"> | |
| 19 <param name="bed_vs_interval_selector" type="select" label="Intersect with BED dataset or an interval"> | |
| 20 <option value="bed">BED</option> | |
| 21 <option value="interval">Interval</option> | |
| 22 </param> | |
| 23 <when value="bed"> | |
| 24 <param name="bed_input" type="data" format="bed" label="Select BED dataset" /> | |
| 25 </when> | |
| 26 <when value="interval"> | |
| 27 <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" /> | |
| 28 </when> | |
| 29 </conditional> | |
| 30 <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." /> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="vcf" name="out_file1" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="bed_vs_interval_selector" value="bed" /> | |
| 38 <param name="bed_input" value="vcfannotate.bed" /> | |
| 39 <param name="invert" value="False" /> | |
| 40 <param name="vcf_input" value="vcflib.vcf"/> | |
| 41 <output name="out_file1" file="vcfbedintersect-test1.vcf"/> | |
| 42 </test> | |
| 43 <test> | |
| 44 <param name="bed_vs_interval_selector" value="interval" /> | |
| 45 <param name="int_input" value="20:1-30000" /> | |
| 46 <param name="invert" value="False" /> | |
| 47 <param name="vcf_input" value="vcflib.vcf"/> | |
| 48 <output name="out_file1" file="vcfbedintersect-test2.vcf"/> | |
| 49 </test> | |
| 50 </tests> | |
| 51 | |
| 52 <help> | |
| 53 | |
| 54 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). | |
| 55 | |
| 56 ---- | |
| 57 | |
| 58 VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 59 | |
| 60 </help> | |
| 61 </tool> |