Mercurial > repos > devteam > vcfannotategenotypes
view vcfannotategenotypes.xml @ 4:84959112d9a6 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 08:04:28 -0500 |
parents | 70bc6ced57f7 |
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<tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="@WRAPPER_VERSION@+galaxy0"> <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>