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minfi_dropsnp.xml |
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| diff -r a63802ce1d26 -r 3eae88629318 minfi_dropsnp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_dropsnp.xml Fri Feb 22 11:16:23 2019 -0500 |
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| @@ -0,0 +1,45 @@ +<tool id="minfi_dropsnp" name="Minfi drop SNPs" version="@MINFI_VERSION@"> + <description>drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> +<requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement> + </expand> + <command detect_errors="exit_code"> + <![CDATA[ + Rscript '$minfi_snp_script' + ]]> + </command> + <configfiles> + <configfile name="minfi_snp_script"><![CDATA[ +require("minfi", quietly = TRUE) + +GRSet <- get(load('$grset')) + +GRSet <- dropLociWithSnps(GRSet, snps=c("SBE","CpG"), maf=0) + +save(GRSet,file = '$grsetwithoutsnp') + ]]> + </configfile> + </configfiles> + <inputs> + <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic +location."/> + </inputs> + <outputs> + <data name="grsetwithoutsnp" format="rdata" from_work_dir="dropsnpGRSet.rdata" label="GRSet without SNPs"/> + </outputs> + <tests> + <test> + <param name="grset" value="GRSet.rdata"/> + <output name="grsetwithoutsnp" file="GRSet_without_SNPs.rdata"/> + </test> + </tests> + <help><![CDATA[ +This tool is a version of the dropLociWithSnps function adapted to drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension (recommend). + +The output is a GenomicRatioSet object without SNPs loci. + ]]></help> + <expand macro="citations" /> +</tool> |