Mercurial > repos > devteam > vcfbedintersect
changeset 2:31a86dbe17c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbedintersect commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:08:06 -0400 |
| parents | 834e1f313036 |
| children | 9edfe5145ba8 |
| files | macros.xml tool_dependencies.xml vcfbedintersect.xml |
| diffstat | 3 files changed, 61 insertions(+), 69 deletions(-) [+] |
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--- a/macros.xml Wed Nov 11 12:58:07 2015 -0500 +++ b/macros.xml Thu Sep 15 16:08:06 2016 -0400 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8a5602bf07">vcflib</requirement> + <requirement type="package" version="1.0.0_rc1">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,6 +10,7 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> <xml name="citations"> <citations> <citation type="bibtex">
--- a/tool_dependencies.xml Wed Nov 11 12:58:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="vcflib" version="8a5602bf07"> - <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/vcfbedintersect.xml Wed Nov 11 12:58:07 2015 -0500 +++ b/vcfbedintersect.xml Thu Sep 15 16:08:06 2016 -0400 @@ -1,62 +1,59 @@ -<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> +<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>