Mercurial > repos > devteam > vcfbedintersect
view vcfbedintersect.xml @ 1:300910e82a2c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author | devteam |
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date | Thu, 15 Sep 2016 16:06:10 -0400 |
parents | 8a7c833c4527 |
children | b886d025cc05 |
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<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="@WRAPPER_VERSION@.0"> <description>Intersect VCF and BED datasets</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio" /> <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="BED dataset or an interval to intersect with"> <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" 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" ftype="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> <expand macro="citations" /> </tool>