Mercurial > repos > anton > vcfbedintersect
diff vcfbedintersect.xml @ 0:7e8a201b4c1c
Imported from capsule None
author | anton |
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date | Wed, 11 Jun 2014 17:11:32 -0400 |
parents | |
children | a83d472202c8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfbedintersect.xml Wed Jun 11 17:11:32 2014 -0400 @@ -0,0 +1,61 @@ +<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.1"> +<requirements> + <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> + <!-- <requirement type="package" version="0.1.18">samtools</requirement> --> +</requirements> + <description>Intersect VCF and BED datasets</description> + <command> + #if str($bed_vs_interval.bed_vs_interval_selector) == "bed": + vcfintersect -b "${bed_vs_interval.bed_input}" ${invert} "${vcf_input}" > "${out_file1}" + #else: + vcfintersect -R "${bed_vs_interval.int_input}" ${invert} "${vcf_input}" > "${out_file1}" + #end if + + </command> + <inputs> + <!-- selecting refernce source --> + <param name="vcf_input" type="data" format="vcf" label="Select VCF dataset" /> + <conditional name="bed_vs_interval"> + <param name="bed_vs_interval_selector" type="select" label="Intersect with BED dataset or an interval"> + <option value="bed">BED</option> + <option value="interval">Interval</option> + </param> + <when value="bed"> + <param name="bed_input" type="data" format="bed" label="Select BED dataset" /> + </when> + <when value="interval"> + <param name="int_input" type="text" size="20" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" /> + </when> + </conditional> + <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert. Print entries that DO NOT intersect." /> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="bed_vs_interval_selector" value="bed" /> + <param name="bed_input" value="vcfannotate.bed" /> + <param name="invert" value="False" /> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbedintersect-test1.vcf"/> + </test> + <test> + <param name="bed_vs_interval_selector" value="interval" /> + <param name="int_input" value="20:1-30000" /> + <param name="invert" value="False" /> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbedintersect-test2.vcf"/> + </test> + </tests> + + <help> + +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). + +---- + +VCFBEDintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + +</help> +</tool>