Mercurial > repos > devteam > vcfhethom
changeset 1:4d7bf6277295 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfhethom commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:05:37 -0400 |
| parents | 1de250ea8c1a |
| children | d3482e14d5a4 |
| files | macros.xml test-data/vcfhethom-test2.tab tool_dependencies.xml vcfhethom.xml |
| diffstat | 4 files changed, 64 insertions(+), 70 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Mon Nov 09 12:33:06 2015 -0500 +++ b/macros.xml Thu Sep 15 16:05:37 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/vcfhethom-test2.tab Mon Nov 09 12:33:06 2015 -0500 +++ b/test-data/vcfhethom-test2.tab Thu Sep 15 16:05:37 2016 -0400 @@ -1,2 +1,2 @@ NA00001 NA00002 NA00003 -inf inf 1 +inf inf 0.75
--- a/tool_dependencies.xml Mon Nov 09 12:33:06 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/vcfhethom.xml Mon Nov 09 12:33:06 2015 -0500 +++ b/vcfhethom.xml Thu Sep 15 16:05:37 2016 -0400 @@ -1,62 +1,61 @@ -<tool id="vcfhethom" name="VCFhetHomAlleles:" version="0.0.3"> - <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command> - - #if str($analysis_type) == "count": - vcfhetcount "${vcf_input}" > "${out_file1}" - #elif str($analysis_type) == "ratio": - vcfhethomratio "${vcf_input}" > "${out_file1}" - #elif str($analysis_type) == "allele_count": - vcfcountalleles "${vcf_input}" > "${out_file1}" - #end if - -</command> - - <inputs> - <param name="analysis_type" type="select" display="radio" label="Select type of calculation:"> - <option value="count">Compute the number of heterozygotes</option> - <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option> - <option value="allele_count">Compute the total number of alleles</option> - </param> - <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="analysis_type" value="count"/> - <param name="vcf_input" value="vcflib.vcf"/> - <output name="out_file1" file="vcfhethom-test1.tab"/> - </test> - <test> - <param name="analysis_type" value="ratio"/> - <param name="vcf_input" value="vcflib.vcf"/> - <output name="out_file1" file="vcfhethom-test2.tab"/> - </test> - <test> - <param name="analysis_type" value="allele_count"/> - <param name="vcf_input" value="vcflib.vcf"/> - <output name="out_file1" file="vcfhethom-test3.tab"/> - </test> - </tests> - <help> - -This tool performs three basic calculations: - -(1) Computes the number of heterozygotes -(2) Computes the ratio between heterozygotes and homozygotes -(3) Computes the total number of alleles in the input dataset - ----- - -This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). - -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfhethom" name="VCFhetHomAlleles:" version="@WRAPPER_VERSION@.0"> + <description>Count the number of heterozygotes and alleles, compute het/hom ratio</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command> + + #if str($analysis_type) == "count": + vcfhetcount "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "ratio": + vcfhethomratio "${vcf_input}" > "${out_file1}" + #elif str($analysis_type) == "allele_count": + vcfcountalleles "${vcf_input}" > "${out_file1}" + #end if + + </command> + <inputs> + <param name="analysis_type" type="select" display="radio" label="Select type of calculation:"> + <option value="count">Compute the number of heterozygotes</option> + <option value="ratio">Compute the ratio between heterozygotes and homozygotes</option> + <option value="allele_count">Compute the total number of alleles</option> + </param> + <param format="vcf" name="vcf_input" type="data" label="In this VCF dataset"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="analysis_type" value="count"/> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfhethom-test1.tab"/> + </test> + <test> + <param name="analysis_type" value="ratio"/> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfhethom-test2.tab"/> + </test> + <test> + <param name="analysis_type" value="allele_count"/> + <param name="vcf_input" value="vcflib.vcf"/> + <output name="out_file1" file="vcfhethom-test3.tab"/> + </test> + </tests> + <help> + +This tool performs three basic calculations: + +(1) Computes the number of heterozygotes +(2) Computes the ratio between heterozygotes and homozygotes +(3) Computes the total number of alleles in the input dataset + +---- + +This tools is based on vcfhetcount, vcfhethomratio,and vcfcountalleles utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + +</help> + <expand macro="citations" /> +</tool>