Mercurial > repos > anton > vcffixup
comparison vcffixup.xml @ 0:07ef509fddbb
Imported from capsule None
| author | anton |
|---|---|
| date | Wed, 11 Jun 2014 17:10:26 -0400 |
| parents | |
| children | ad5153826912 |
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| -1:000000000000 | 0:07ef509fddbb |
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| 1 <tool id="vcffixup" name="VCFfixup:" version="0.0.1"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> | |
| 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 | |
| 21 Uses genotypes from the VCF file to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records. | |
| 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> |