Mercurial > repos > devteam > vcfbedintersect
diff vcfbedintersect.xml @ 0:8a7c833c4527 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 12:29:56 -0500 |
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children | 300910e82a2c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfbedintersect.xml Mon Nov 09 12:29:56 2015 -0500 @@ -0,0 +1,62 @@ +<tool id="vcfbedintersect" name="VCF-BEDintersect:" version="0.0.3"> + <description>Intersect VCF and BED datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <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" /> + <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>