Mercurial > repos > devteam > vcfflatten
changeset 1:5fe607441f62 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:04:07 -0400 |
| parents | ac725e729ac6 |
| children | 5f4be9e020d9 |
| files | macros.xml tool_dependencies.xml vcfflatten.xml |
| diffstat | 3 files changed, 32 insertions(+), 37 deletions(-) [+] |
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--- a/macros.xml Mon Nov 09 12:32:13 2015 -0500 +++ b/macros.xml Thu Sep 15 16:04:07 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 Mon Nov 09 12:32:13 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/vcfflatten.xml Mon Nov 09 12:32:13 2015 -0500 +++ b/vcfflatten.xml Thu Sep 15 16:04:07 2016 -0400 @@ -1,30 +1,30 @@ -<tool id="vcfflatten2" name="VCFflatten:" version="0.0.3"> - <description>Removes multi-allelic sites by picking the most common alternate</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcfflatten "${input1}" > "${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="vcfflatten-input1.vcf"/> - <output name="out_file1" file="vcfflatten-test1.vcf"/> - </test> - </tests> - <help> - -Removes multi-allelic sites by picking the most common alternate. Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype. - ----- - -Vcfflatten @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfflatten2" name="VCFflatten:" version="@WRAPPER_VERSION@.0"> + <description>Removes multi-allelic sites by picking the most common alternate</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcfflatten "${input1}" > "${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="vcfflatten-input1.vcf"/> + <output name="out_file1" file="vcfflatten-test1.vcf"/> + </test> + </tests> + <help> + +Removes multi-allelic sites by picking the most common alternate. Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype. + +---- + +Vcfflatten @IS_PART_OF_VCFLIB@ +</help> + <expand macro="citations" /> +</tool>