Mercurial > repos > devteam > vcfbedintersect
annotate vcfbedintersect.xml @ 1:834e1f313036 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:58:07 -0500 |
| parents | 8a482a9aa45d |
| children | 31a86dbe17c0 |
| rev | line source |
|---|---|
| 0 | 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"> | |
|
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834e1f313036
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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28 <param name="int_input" type="text" value="chr20:1-30" label="Enter interval string" help="use chr:start-end format" /> |
| 0 | 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> |