Mercurial > repos > devteam > vcfannotategenotypes
view vcfannotategenotypes.xml @ 2:c96a7e49150a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author | devteam |
---|---|
date | Thu, 15 Sep 2016 16:07:50 -0400 |
parents | ad57b4feaf87 |
children | 70bc6ced57f7 |
line wrap: on
line source
<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>