Mercurial > repos > devteam > vcfgenotypes
changeset 1:30963674e8fd draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfgenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:05:15 -0400 |
| parents | a1a3b63d2af2 |
| children | fb7560e94faa |
| files | macros.xml test-data/vcfgenotypes-test1.tab tool_dependencies.xml vcfgenotypes.xml |
| diffstat | 4 files changed, 33 insertions(+), 38 deletions(-) [+] |
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--- a/macros.xml Mon Nov 09 12:32:49 2015 -0500 +++ b/macros.xml Thu Sep 15 16:05:15 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/test-data/vcfgenotypes-test1.tab Mon Nov 09 12:32:49 2015 -0500 +++ b/test-data/vcfgenotypes-test1.tab Thu Sep 15 16:05:15 2016 -0400 @@ -5,5 +5,5 @@ 20 1110696 A G,T A,G,T NA00001:G/T NA00002:T/G NA00003:T/T 20 1230237 T . T,. NA00001:T/T NA00002:T/T NA00003:T/T 20 1234567 G GA,GAC G,GA,GAC NA00001:G/GA NA00002:G/GAC NA00003:GA/GA -20 1235237 T . T,. NA00001:T/T NA00002:T/T +20 1235237 T . T,. NA00001:T/T NA00002:T/T NA00003:T/T X 10 AC A,ATG AC,A,ATG NA00001:AC NA00002:AC/A NA00003:AC/ATG
--- a/tool_dependencies.xml Mon Nov 09 12:32:49 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="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/vcfgenotypes.xml Mon Nov 09 12:32:49 2015 -0500 +++ b/vcfgenotypes.xml Thu Sep 15 16:05:15 2016 -0400 @@ -1,30 +1,30 @@ -<tool id="vcfgenotypes" name="VCFgenotypes:" version="0.0.3"> - <description>Convert numerical representation of genotypes to allelic</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcfgenotypes "${vcf_input}" > "${out_file1}"</command> - <inputs> - <param format="vcf" name="vcf_input" type="data" label="Select VCF dataset"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="vcf_input" value="vcflib.vcf"/> - <output name="out_file1" file="vcfgenotypes-test1.tab"/> - </test> - </tests> - <help> - -Converts numerical representation of genotypes (standard in GT field) to the alleles provided in the call's ALT/REF fields. - ----- - -Vcfgenotypes @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfgenotypes" name="VCFgenotypes:" version="@WRAPPER_VERSION@.0"> + <description>Convert numerical representation of genotypes to allelic</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcfgenotypes "${vcf_input}" > "${out_file1}"</command> + <inputs> + <param format="vcf" name="vcf_input" type="data" label="Select VCF dataset"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfgenotypes-test1.tab"/> + </test> + </tests> + <help> + +Converts numerical representation of genotypes (standard in GT field) to the alleles provided in the call's ALT/REF fields. + +---- + +Vcfgenotypes @IS_PART_OF_VCFLIB@ +</help> + <expand macro="citations" /> +</tool>