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minfi_dmp.xml |
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| diff -r 491cf4ada3a3 -r cffa2871fe8b minfi_dmp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/minfi_dmp.xml Fri Feb 22 08:15:47 2019 -0500 |
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| @@ -0,0 +1,97 @@ +<tool id="minfi_dmp" name="Minfi DMP" version="@MINFI_VERSION@"> + <description>to find differentially methylated positions</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$minfi_dmp_script' + ]]></command> + <configfiles> + <configfile name="minfi_dmp_script"><![CDATA[ +require("minfi", quietly = TRUE) + +set <- get(load('$grset')) + +genomeranges <- as.data.frame(ranges(set)) + +beta <- getBeta(set) + +pheno <- read.table('$phenotype_table',skip=1) + +type <- '$phenotype' + +qCutoff <- as.numeric('$q_cutoff') + +shrinkVar <- '$variance_shrinkage' + +tab <- read.table('$ucsc_genome') + +tab <- tab[,-(11:14),drop=FALSE] + +colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names") + +tab[,"source"] <- NULL + +tab[,"frame"] <- NULL + +tab[,"attributes"] <- NULL + +dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar) + +dmp[,"names"] <- rownames(dmp) + +data <- merge(dmp, tab, by="names",sort = TRUE) + +data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")] + +write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t") + ]]> + </configfile> + </configfiles> + <inputs> + <param type="data" name="grset" format="rdata" label="Input Set" help="MethylSet, RatioSet or GenomicRatioSet" /> + <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"/> + <param name="phenotype" type="select" label="Phenotype Type"> + <option value="categorical">categorical</option> + <option value="continuous">continuous</option> + </param> + <param name="q_cutoff" type="integer" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/> + <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage" + help="Enable variance shrinkage is recommended when sample sizes are small"/> + <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/> + </inputs> + <outputs> + <data name="dmp" format="interval" label="Differentially Methylated Positions"/> + </outputs> + <tests> + <test> + <param name="grset" value="GRSet_without_SNPs.rdata"/> + <param name="phenotype_table" value="phenotypeTable.txt"/> + <param name="phenotype" value="categorical"/> + <param name="q_cutoff" value="1"/> + <param name="variance_shrinkage" value="FALSE"/> + <param name="ucsc_genome" value="ucsc.gtf"/> + <output name="dmp" file="Differentially_Methylated_Positions.interval"/> + </test> + </tests> + <help><![CDATA[ +This tool creates differentially methylated positions (DMPs) with respect to a phenotype covariate. The phenotype may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure). + +The output is an interval file with the following columns: + + - seqnames + - start + - end + - cpg + - names + - score + - strand + - feature + - intercept + - f pval + - qval + + ]]></help> + <expand macro="citations" /> +</tool> |