Mercurial > repos > devteam > vcfannotategenotypes
comparison vcfannotategenotypes.xml @ 0:7a32e4b43579 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 12:29:39 -0500 |
| parents | |
| children | 9c9969071728 |
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| -1:000000000000 | 0:7a32e4b43579 |
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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" 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> |