| Previous changeset 1:ad57b4feaf87 (2015-11-11) Next changeset 3:70bc6ced57f7 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcfannotategenotypes-test1.vcf vcfannotategenotypes.xml |
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removed:
tool_dependencies.xml |
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| diff -r ad57b4feaf87 -r c96a7e49150a macros.xml --- a/macros.xml Wed Nov 11 12:57:55 2015 -0500 +++ b/macros.xml Thu Sep 15 16:07:50 2016 -0400 |
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| @@ -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"> |
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| diff -r ad57b4feaf87 -r c96a7e49150a test-data/vcfannotategenotypes-test1.vcf --- a/test-data/vcfannotategenotypes-test1.vcf Wed Nov 11 12:57:55 2015 -0500 +++ b/test-data/vcfannotategenotypes-test1.vcf Thu Sep 15 16:07:50 2016 -0400 |
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| @@ -29,5 +29,5 @@ 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1/2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0/0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1 -20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. . +20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:. X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2 |
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| diff -r ad57b4feaf87 -r c96a7e49150a tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:57:55 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r ad57b4feaf87 -r c96a7e49150a vcfannotategenotypes.xml --- a/vcfannotategenotypes.xml Wed Nov 11 12:57:55 2015 -0500 +++ b/vcfannotategenotypes.xml Thu Sep 15 16:07:50 2016 -0400 |
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| @@ -1,34 +1,34 @@ -<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3"> - <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/> - <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/> - <param name="tag_option" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="tag_option" value="added-genotypes"/> - <param name="input1" value="vcflib.vcf"/> - <param name="input2" value="vcfannotategenotypes-input2.vcf"/> - <output name="out_file1" file="vcfannotategenotypes-test1.vcf" /> - </test> - </tests> -<help> - -Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation. Also adds a 'has\_variant' flag for sites where the second file has a variant. - ------ - -Vcfannotate @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="@WRAPPER_VERSION@.0"> + <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/> + <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/> + <param name="tag_option" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="tag_option" value="added-genotypes"/> + <param name="input1" value="vcflib.vcf"/> + <param name="input2" value="vcfannotategenotypes-input2.vcf"/> + <output name="out_file1" file="vcfannotategenotypes-test1.vcf" /> + </test> + </tests> +<help> + +Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation. Also adds a 'has\_variant' flag for sites where the second file has a variant. + +----- + +Vcfannotate @IS_PART_OF_VCFLIB@ +</help> + <expand macro="citations" /> +</tool> |