Mercurial > repos > devteam > vcfcombine
changeset 2:18f9f2624bd6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcombine commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:04:40 -0400 |
| parents | 55ca04702702 |
| children | 53edb91ed051 |
| files | macros.xml test-data/vcfcombine-test1.vcf tool_dependencies.xml vcfcombine.xml |
| diffstat | 4 files changed, 42 insertions(+), 48 deletions(-) [+] |
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--- a/macros.xml Wed Nov 11 12:58:45 2015 -0500 +++ b/macros.xml Thu Sep 15 16:04:40 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/vcfcombine-test1.vcf Wed Nov 11 12:58:45 2015 -0500 +++ b/test-data/vcfcombine-test1.vcf Thu Sep 15 16:04:40 2016 -0400 @@ -27,5 +27,5 @@ 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2 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;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;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 -20 1235237 . T . 0 . . GT 0/0 0|0 . +20 1235237 . T . 0 . . GT 0/0 0|0 ./. X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2
--- a/tool_dependencies.xml Wed Nov 11 12:58:45 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/vcfcombine.xml Wed Nov 11 12:58:45 2015 -0500 +++ b/vcfcombine.xml Thu Sep 15 16:04:40 2016 -0400 @@ -1,40 +1,39 @@ -<tool id="vcfcombine" name="VCFcombine:" version="0.0.4"> - <description>Combine multiple VCF datasets</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command> - - vcfcombine - - #for $input_vcf in $input_vcfs: - "${input_vcf}" - #end for - - > "${out_file1}" - - </command> - <inputs> - <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input_vcfs" value="vcflib.vcf"/> - <output name="out_file1" file="vcfcombine-test1.vcf"/> - </test> - </tests> - <help> - -Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted. - ------ - -Vcfcombine @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfcombine" name="VCFcombine:" version="@WRAPPER_VERSION@.0"> + <description>Combine multiple VCF datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command> + vcfcombine + + #for $input_vcf in $input_vcfs: + "${input_vcf}" + #end for + + > "${out_file1}" + + </command> + <inputs> + <param name="input_vcfs" type="data" format="vcf" label="Select VCF Datasets" min="2" multiple="True"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input_vcfs" value="vcflib.vcf,vcflib.vcf" ftype="vcf"/> + <output name="out_file1" file="vcfcombine-test1.vcf"/> + </test> + </tests> + <help> + +Combines VCF files positionally, combining samples when sites and alleles are identical. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files, which are combined when records in multiple files match. Alleles must have identical ordering to be combined into one record. If they do not, multiple records will be emitted. + +----- + +Vcfcombine @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool>