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1 <tool id="vcf_annotate" name="Annotate" version="1.0.0">
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2 <description>a VCF file (dbSNP, hapmap)</description>
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3 <command interpreter="python">
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4 vcfPytools.py
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5 annotate
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6 --in=$input1
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7 #if $annotation_options.annotate == "dbsnp"
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8 --dbsnp=$input2
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9 #elif $annotation_options.annotate == "hapmap"
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10 --hapmap=$input2
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11 #end if
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12 --out=$output1
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13 </command>
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14 <inputs>
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15 <param name="input1" label="VCF file to annotate" type="data" format="vcf" />
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16 <conditional name="annotation_options">
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17 <param name="annotate" type="select" label="annotation source">
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18 <option value="dbsnp">dbSNP vcf file</option>
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19 <option value="hapmap">hapmap vcf file</option>
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20 </param>
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21 <when value="dbsnp">
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22 <param name="input2" label="dbSNP vcf file" type="data" format="vcf" help="This option will annotate the vcf file with dbSNP rsid values. The input dbSNP file must also be in vcf v4.0 format. Only dbSNP entries with VC=SNP are included."/>
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23 </when>
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24 <when value="hapmap">
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25 <param name="input2" label="hapmap vcf file" type="data" format="vcf" help="This option will annotate the vcf file info string to include HM3 if the record is included hapmap. If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A."/>
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26 </when>
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27 </conditional>
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28 </inputs>
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29 <outputs>
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30 <data format="vcf" name="output1" label="${tool.name} ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input1" value="test.small.vcf" ftype="vcf" />
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35 <param name="annotate" value="dbsnp" />
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36 <param name="input2" value="dbsnp.small.vcf" ftype="vcf" />
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37 <output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" />
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38 </test>
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39 <test>
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40 <param name="input1" value="test.small.vcf" ftype="vcf" />
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41 <param name="annotate" value="hapmap" />
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42 <param name="input2" value="hapmap.small.vcf" ftype="vcf" />
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43 <output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" />
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44 </test>
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45 </tests>
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46 <help>
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47
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48 **What it does**
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49
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50 This tool uses vcfPytools_' annotate command annotate a VCF file
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51
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52 .. _vcfPytools: https://github.com/AlistairNWard/vcfPytools
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53
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54 Currently, either a hapmap or a dbsnp file should be provided, not both.
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55
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56 dbSNP option will annotate the VCF file with dbSNP rsid values. The input dbSNP file must also be in VCF v4.0 format. Only dbSNP entries with VC=SNP are included.
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57
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58 hapmap option will annotate the VCF file info string to include HM3 if the record is included hapmap. If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A.
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59
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60
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61 </help>
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62 </tool> |
