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1 <tool id="vcffixup" name="VCFfixup:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 </requirements>
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5 <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
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6 <command>vcffixup "${input1}" > "${out_file1}"</command>
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7 <inputs>
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8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
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9 </inputs>
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10 <outputs>
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11 <data format="vcf" name="out_file1" />
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input1" value="vcflib.vcf"/>
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16 <output name="out_file1" file="vcffixup-test1.vcf"/>
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17 </test>
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18 </tests>
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19 <help>
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20
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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.
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22
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23 ----
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24
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25 Vcffixup is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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26
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27 </help>
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28 </tool>
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