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1 <tool id="vcfannotategenotypes" name="VCFannotateGenotypes:" version="0.0.3">
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2 <description>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset</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>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
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9 <inputs>
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10 <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
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11 <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>
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12 <param name="tag_option" size="20" type="text" value="added-genotypes" label="Mark genotypes added to the first dataset with this tag" help="Annotation tag"/>
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13 </inputs>
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14 <outputs>
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15 <data format="vcf" name="out_file1" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="tag_option" value="added-genotypes"/>
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20 <param name="input1" value="vcflib.vcf"/>
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21 <param name="input2" value="vcfannotategenotypes-input2.vcf"/>
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22 <output name="out_file1" file="vcfannotategenotypes-test1.vcf" />
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23 </test>
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24 </tests>
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25 <help>
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26
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27 Annotates genotypes in the **First** dataset with genotypes from the **Second** adding the genotype as another flag to each sample filled in the first file. **Annotation-tag** is the name of the sample flag which is added to store the annotation. Also adds a 'has\_variant' flag for sites where the second file has a variant.
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28
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29 -----
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30
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31 Vcfannotate @IS_PART_OF_VCFLIB@
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32 </help>
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33 <expand macro="citations" />
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34 </tool>
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