/tools/vcf_tools/annotate.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 62 lines · 54 code · 8 blank · 0 comment · 0 complexity · 51d0540ea80f4b18ff515bfe78f8323e MD5 · raw file
- <tool id="vcf_annotate" name="Annotate" version="1.0.0">
- <description>a VCF file (dbSNP, hapmap)</description>
- <command interpreter="python">
- vcfPytools.py
- annotate
- --in=$input1
- #if $annotation_options.annotate == "dbsnp"
- --dbsnp=$input2
- #elif $annotation_options.annotate == "hapmap"
- --hapmap=$input2
- #end if
- --out=$output1
- </command>
- <inputs>
- <param name="input1" label="VCF file to annotate" type="data" format="vcf" />
- <conditional name="annotation_options">
- <param name="annotate" type="select" label="annotation source">
- <option value="dbsnp">dbSNP vcf file</option>
- <option value="hapmap">hapmap vcf file</option>
- </param>
- <when value="dbsnp">
- <param name="input2" label="dbSNP vcf file" type="data" format="vcf" help="This option will annotate the vcf file with dbSNP rsid values. The input dbSNP file must also be in vcf v4.0 format. Only dbSNP entries with VC=SNP are included."/>
- </when>
- <when value="hapmap">
- <param name="input2" label="hapmap vcf file" type="data" format="vcf" help="This option will annotate the vcf file info string to include HM3 if the record is included hapmap. If the ref/alt values do not match the hapmap file, the info string will be populated with HM3A."/>
- </when>
- </conditional>
- </inputs>
- <outputs>
- <data format="vcf" name="output1" label="${tool.name} ${on_string}" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="test.small.vcf" ftype="vcf" />
- <param name="annotate" value="dbsnp" />
- <param name="input2" value="dbsnp.small.vcf" ftype="vcf" />
- <output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" />
- </test>
- <test>
- <param name="input1" value="test.small.vcf" ftype="vcf" />
- <param name="annotate" value="hapmap" />
- <param name="input2" value="hapmap.small.vcf" ftype="vcf" />
- <output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" />
- </test>
- </tests>
- <help>
- **What it does**
- This tool uses vcfPytools_' annotate command annotate a VCF file
- .. _vcfPytools: https://github.com/AlistairNWard/vcfPytools
- Currently, either a hapmap or a dbsnp file should be provided, not both.
- 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.
- 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.
- </help>
- </tool>