Mercurial > repos > anton > vcfannotategenotypes

comparison vcfannotategenotypes.xml @ 3:9baa80088ab6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author anton
date Mon, 15 Sep 2014 14:48:52 -0400
parents 846a4449a50a
children
comparison
equal deleted inserted replaced
2:846a4449a50a 3:9baa80088ab6
1 <tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.2"> 1 <tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="86723982aa">vcflib</requirement> 3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
4 </requirements> 4 </requirements>
5 <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description> 5 <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
6 <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command> 6 <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
7 <inputs> 7 <inputs>
8 <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/> 8 <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
20 <output name="out_file1" file="vcfannotategenotypes-test1.vcf" /> 20 <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
21 </test> 21 </test>
22 </tests> 22 </tests>
23 <help> 23 <help>
24 24
25 Annotates genotypes in the **First** file with genotypes in the **Second** adding the genotype as another flag to each sample filed 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. 25 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.
26 26
27 ----- 27 -----
28 28
29 Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 29 Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
30 30