Mercurial > repos > lecorguille > camera_annotate
view CAMERA.r @ 15:6139bfcc95cb draft
planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
author | lecorguille |
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date | Thu, 01 Mar 2018 08:29:32 -0500 |
parents | 1c30ff90f3ae |
children | a2c49996603e |
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#!/usr/bin/env Rscript # CAMERA.r version="2.2.1" # ----- PACKAGE ----- cat("\tPACKAGE INFO\n") setRepositories(graphics=F, ind=31) #pkgs=c("xcms","batch") pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch") for(p in pkgs) { suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) cat(p,"\t",as.character(packageVersion(p)),"\n",sep="") } source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } cat("\n\n"); # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') cat("\n\n"); # ----- PROCESSING INFILE ----- cat("\tINFILE PROCESSING INFO\n") #image is an .RData file necessary to use xset variable given by previous tools if (!is.null(listArguments[["image"]])){ load(listArguments[["image"]]); listArguments[["image"]]=NULL } if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) { load(listArguments[["image_pos"]]) xaP=xa listOFlistArgumentsP=listOFlistArguments if (exists("xsAnnotate_object")) xaP=xsAnnotate_object diffrepP=NULL if (exists("diffrep")) diffrepP=diffrep load(listArguments[["image_neg"]]) xaN=xa listOFlistArgumentsN=listOFlistArguments if (exists("xsAnnotate_object")) xaN=xsAnnotate_object diffrepN=NULL if (exists("diffrep")) diffrepN=diffrep } cat("\n\n") # ----- ARGUMENTS PROCESSING ----- cat("\tARGUMENTS PROCESSING INFO\n") # Save arguments to generate a report if (!exists("listOFlistArguments")) listOFlistArguments=list() listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments #saving the commun parameters thefunction = listArguments[["xfunction"]] listArguments[["xfunction"]]=NULL #delete from the list of arguments xsetRdataOutput = paste(thefunction,"RData",sep=".") if (!is.null(listArguments[["xsetRdataOutput"]])){ xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL } rplotspdf = "Rplots.pdf" if (!is.null(listArguments[["rplotspdf"]])){ rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL } dataMatrixOutput = "dataMatrix.tsv" if (!is.null(listArguments[["dataMatrixOutput"]])){ dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL } variableMetadataOutput = "variableMetadata.tsv" if (!is.null(listArguments[["variableMetadataOutput"]])){ variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL } #Import the different functions source_local("lib.r") # We unzip automatically the chromatograms from the zip files. if (thefunction %in% c("annotatediff")) { if (!exists("zipfile")) zipfile=NULL if (!exists("singlefile")) singlefile=NULL rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) zipfile = rawFilePath$zipfile singlefile = rawFilePath$singlefile listArguments = rawFilePath$listArguments directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) } #addition of xset object to the list of arguments in the first position if (exists("xset") != 0){ listArguments=append(list(xset), listArguments) } cat("\n\n") # ----- PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") #change the default display settings pdf(file=rplotspdf, width=16, height=12) if (thefunction %in% c("annotatediff")) { results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput) xa=results_list[["xa"]] diffrep=results_list[["diffrep"]] variableMetadata=results_list[["variableMetadata"]] cat("\n\n") cat("\tXSET OBJECT INFO\n") print(xa) } if (thefunction %in% c("combinexsAnnos")) { cAnnot=combinexsAnnos_function( xaP=xaP,xaN=xaN, listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN, diffrepP=diffrepP,diffrepN=diffrepN, pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]], convertRTMinute=listArguments[["convertRTMinute"]], numDigitsMZ=listArguments[["numDigitsMZ"]], numDigitsRT=listArguments[["numDigitsRT"]], variableMetadataOutput=variableMetadataOutput ) } dev.off() #saving R data in .Rdata file to save the variables used in the present tool objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile","singlefile") save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) cat("\n\n") cat("\tDONE\n")