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1 <tool id="vcffixup" name="VCFfixup:" version="0.0.3">
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2 <description>Count the allele frequencies across alleles present in each record in the VCF file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio" />
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8 <command>vcffixup "${input1}" > "${out_file1}"</command>
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9 <inputs>
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10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
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11 </inputs>
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12 <outputs>
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13 <data format="vcf" name="out_file1" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input1" value="vcflib.vcf"/>
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18 <output name="out_file1" file="vcffixup-test1.vcf"/>
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19 </test>
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20 </tests>
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21 <help>
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22
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23 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.
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24
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25 ----
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26
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27 Vcffixup @IS_PART_OF_VCFLIB@
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28 </help>
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29 <expand macro="citations" />
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30 </tool>
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