Mercurial > repos > anton > vcffixup
annotate vcffixup.xml @ 3:434227302729 draft default tip
Uploaded
| author | anton |
|---|---|
| date | Mon, 15 Sep 2014 14:51:23 -0400 |
| parents | 9f0d84b2deba |
| children |
| rev | line source |
|---|---|
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9f0d84b2deba
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
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diff
changeset
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1 <tool id="vcffixup" name="VCFfixup:" version="0.0.2"> |
| 0 | 2 <requirements> |
| 3 | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Count the allele frequencies across alleles present in each record in the VCF file</description> | |
| 6 <command>vcffixup "${input1}" > "${out_file1}"</command> | |
| 7 <inputs> | |
| 8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data format="vcf" name="out_file1" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input1" value="vcflib.vcf"/> | |
| 16 <output name="out_file1" file="vcffixup-test1.vcf"/> | |
| 17 </test> | |
| 18 </tests> | |
| 19 <help> | |
| 20 | |
| 3 | 21 Uses genotypes from the selected VCF dataset to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. |
| 0 | 22 |
| 23 ---- | |
| 24 | |
| 25 Vcffixup is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 26 | |
| 27 </help> | |
| 28 </tool> |