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comparison vcffixup.xml @ 3:434227302729 draft default tip

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author anton
date Mon, 15 Sep 2014 14:51:23 -0400
parents 9f0d84b2deba
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2:9f0d84b2deba 3:434227302729
1 <tool id="vcffixup" name="VCFfixup:" version="0.0.2"> 1 <tool id="vcffixup" name="VCFfixup:" 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>Count the allele frequencies across alleles present in each record in the VCF file</description> 5 <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
6 <command>vcffixup "${input1}" > "${out_file1}"</command> 6 <command>vcffixup "${input1}" > "${out_file1}"</command>
7 <inputs> 7 <inputs>
8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> 8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
16 <output name="out_file1" file="vcffixup-test1.vcf"/> 16 <output name="out_file1" file="vcffixup-test1.vcf"/>
17 </test> 17 </test>
18 </tests> 18 </tests>
19 <help> 19 <help>
20 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. 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.
22 22
23 ---- 23 ----
24 24
25 Vcffixup is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 25 Vcffixup is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
26 26