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comparison vcfannotategenotypes.xml @ 0:c6be83b8883d draft

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author devteam
date Thu, 19 Mar 2015 12:40:45 -0400
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1 <tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3">
2 <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio" />
8 <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
9 <inputs>
10 <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
11 <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
12 <param name="tag_option" size="20" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
13 </inputs>
14 <outputs>
15 <data format="vcf" name="out_file1" />
16 </outputs>
17 <tests>
18 <test>
19 <param name="tag_option" value="added-genotypes"/>
20 <param name="input1" value="vcflib.vcf"/>
21 <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
22 <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
23 </test>
24 </tests>
25 <help>
26
27 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.
28
29 -----
30
31 Vcfannotate @IS_PART_OF_VCFLIB@
32 </help>
33 <expand macro="citations" />
34 </tool>