Mercurial > repos > devteam > vcffixup
changeset 1:9d7e64e4b9fc draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffixup commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:05:59 -0400 |
| parents | a03f346b6aae |
| children | fc5a64fdd5b2 |
| files | macros.xml test-data/vcffixup-test1.vcf tool_dependencies.xml vcffixup.xml |
| diffstat | 4 files changed, 33 insertions(+), 38 deletions(-) [+] |
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--- a/macros.xml Thu Mar 19 14:30:34 2015 -0400 +++ b/macros.xml Thu Sep 15 16:05:59 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/vcffixup-test1.vcf Thu Mar 19 14:30:34 2015 -0400 +++ b/test-data/vcffixup-test1.vcf Thu Sep 15 16:05:59 2016 -0400 @@ -27,5 +27,5 @@ 20 1110696 rs6040355 A G,T 67 PASS AA=T;AC=2,4;AF=0.333333,0.666667;AN=6;DP=10;NS=3;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. 20 1230237 . T . 47 PASS AA=T;AC=0;AF=0;AN=6;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AF=0.5,0.166667;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -20 1235237 . T . 0 . AC=0;AF=0;AN=4;NS=2 GT 0/0 0|0 . +20 1235237 . T . 0 . AC=0;AF=0;AN=4;NS=3 GT 0/0 0|0 ./. X 10 rsTest AC A,ATG 10 PASS AC=1,1;AF=0.2,0.2;AN=5;NS=3 GT 0 0/1 0|2
--- a/tool_dependencies.xml Thu Mar 19 14:30:34 2015 -0400 +++ /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/vcffixup.xml Thu Mar 19 14:30:34 2015 -0400 +++ b/vcffixup.xml Thu Sep 15 16:05:59 2016 -0400 @@ -1,30 +1,30 @@ -<tool id="vcffixup" name="VCFfixup:" version="0.0.3"> - <description>Count the allele frequencies across alleles present in each record in the VCF file</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcffixup "${input1}" > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcffixup-test1.vcf"/> - </test> - </tests> - <help> - -Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. - ----- - -Vcffixup @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcffixup" name="VCFfixup:" version="@WRAPPER_VERSION@.0"> + <description>Count the allele frequencies across alleles present in each record in the VCF file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcffixup "${input1}" > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcffixup-test1.vcf"/> + </test> + </tests> + <help> + +Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. + +---- + +Vcffixup @IS_PART_OF_VCFLIB@ +</help> + <expand macro="citations" /> +</tool>