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62 lines
2.6 KiB
XML
62 lines
2.6 KiB
XML
<tool id="vcf_annotate" name="Annotate" version="1.0.0">
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<description>a VCF file (dbSNP, hapmap)</description>
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<command interpreter="python">
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vcfPytools.py
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annotate
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--in=$input1
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#if $annotation_options.annotate == "dbsnp"
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--dbsnp=$input2
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#elif $annotation_options.annotate == "hapmap"
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--hapmap=$input2
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#end if
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--out=$output1
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</command>
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<inputs>
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<param name="input1" label="VCF file to annotate" type="data" format="vcf" />
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<conditional name="annotation_options">
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<param name="annotate" type="select" label="annotation source">
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<option value="dbsnp">dbSNP vcf file</option>
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<option value="hapmap">hapmap vcf file</option>
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</param>
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<when value="dbsnp">
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<param name="input2" label="dbSNP vcf file" type="data" format="vcf" help="This option will annotate the vcf file with dbSNP rsid values. The input dbSNP file must also be in vcf v4.0 format. Only dbSNP entries with VC=SNP are included."/>
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</when>
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<when value="hapmap">
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<param name="input2" label="hapmap vcf file" type="data" format="vcf" help="This option will annotate the vcf file info string to include HM3 if the record is included hapmap. If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A."/>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="vcf" name="output1" label="${tool.name} ${on_string}" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="test.small.vcf" ftype="vcf" />
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<param name="annotate" value="dbsnp" />
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<param name="input2" value="dbsnp.small.vcf" ftype="vcf" />
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<output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" />
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</test>
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<test>
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<param name="input1" value="test.small.vcf" ftype="vcf" />
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<param name="annotate" value="hapmap" />
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<param name="input2" value="hapmap.small.vcf" ftype="vcf" />
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<output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" />
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</test>
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</tests>
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<help>
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**What it does**
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This tool uses vcfPytools_' annotate command annotate a VCF file
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.. _vcfPytools: https://github.com/AlistairNWard/vcfPytools
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Currently, either a hapmap or a dbsnp file should be provided, not both.
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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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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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</help>
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</tool> |