xcms_retcor: xcms.r annotate

annotate xcms.r @ 6:fcd93f47dcbf draft

planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e

author	lecorguille
date	Thu, 07 Apr 2016 16:04:39 -0400
parents
children	c04568596f40

rev	line source
6 fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	1 #!/usr/bin/env Rscript
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	2 # xcms.r version="2.2.0"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	3 #Authors ABIMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	4 #BPC Addition from Y.guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	5
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	7 # ----- LOG FILE -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	8 log_file=file("log.txt", open = "wt")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	9 sink(log_file)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	10 sink(log_file, type = "output")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	11
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	12
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	13 # ----- PACKAGE -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	14 cat("\tPACKAGE INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	15 #pkgs=c("xcms","batch")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	16 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	17 for(pkg in pkgs) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	18 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	19 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	20 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	21 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	22 cat("\n\n");
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	23
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	24
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	25
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	26
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	27
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	28 # ----- ARGUMENTS -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	29 cat("\tARGUMENTS INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	30 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	31 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	32
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	33 cat("\n\n");
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	34
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	35
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	36 # ----- ARGUMENTS PROCESSING -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	37 cat("\tINFILE PROCESSING INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	38
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	39 #image is an .RData file necessary to use xset variable given by previous tools
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	40 if (!is.null(listArguments[["image"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	41 load(listArguments[["image"]]); listArguments[["image"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	42 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	43
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	44 #Import the different functions
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	45 source_local("lib.r")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	46
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	47 cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	48
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	49 #Import the different functions
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	50
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	51 # ----- PROCESSING INFILE -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	52 cat("\tARGUMENTS PROCESSING INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	53
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	54 # Save arguments to generate a report
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	55 if (!exists("listOFlistArguments")) listOFlistArguments=list()
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	56 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	57
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	58
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	59 #saving the commun parameters
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	60 thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	61
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	62 xsetRdataOutput = paste(thefunction,"RData",sep=".")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	63 if (!is.null(listArguments[["xsetRdataOutput"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	64 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	65 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	66
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	67 rplotspdf = "Rplots.pdf"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	68 if (!is.null(listArguments[["rplotspdf"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	69 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	70 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	71
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	72 sampleMetadataOutput = "sampleMetadata.tsv"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	73 if (!is.null(listArguments[["sampleMetadataOutput"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	74 sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	75 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	76
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	77
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	78
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	79
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	80 if (thefunction %in% c("xcmsSet","retcor")) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	81 ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	82 bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	83 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	84
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	85 #necessary to unzip .zip file uploaded to Galaxy
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	86 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	87
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	88
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	89 if (!is.null(listArguments[["zipfile"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	90 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	91 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	92
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	93 if (!is.null(listArguments[["library"]])){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	94 directory=listArguments[["library"]]; listArguments[["library"]]=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	95 if(!file.exists(directory)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	96 error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	97 print(error_message)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	98 stop(error_message)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	99 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	100 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	101
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	102 # We unzip automatically the chromatograms from the zip files.
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	103 if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	104 if(exists("zipfile") && (zipfile!="")) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	105 if(!file.exists(zipfile)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	106 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	107 print(error_message)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	108 stop(error_message)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	109 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	110
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	111 #list all file in the zip file
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	112 #zip_files=unzip(zipfile,list=T)[,"Name"]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	113
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	114
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	115 #unzip
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	116 suppressWarnings(unzip(zipfile, unzip="unzip"))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	117
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	118 #get the directory name
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	119 filesInZip=unzip(zipfile, list=T);
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	120 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	121 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	122 directory = "."
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	123 if (length(directories) == 1) directory = directories
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	124
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	125 cat("files_root_directory\t",directory,"\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	126
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	127 #
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	128 md5sumList=list("origin"=getMd5sum(directory))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	129
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	130 # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	131 # Remove because can create issue with some clean files
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	132 #@TODO: fix me
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	133 #if (deleteXmlBadCharacters(directory)) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	134 # md5sumList=list("removalBadCharacters"=getMd5sum(directory))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	135 #}
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	136
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	137 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	138 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	139
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	140 #addition of the directory to the list of arguments in the first position
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	141 if (thefunction == "xcmsSet") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	142 checkXmlStructure(directory)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	143 checkFilesCompatibilityWithXcms(directory)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	144 listArguments=append(directory, listArguments)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	145 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	146
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	147
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	148 #addition of xset object to the list of arguments in the first position
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	149 if (exists("xset")){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	150 listArguments=append(list(xset), listArguments)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	151 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	152
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	153 cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	154
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	155
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	156
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	157
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	158
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	159
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	160 # ----- MAIN PROCESSING INFO -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	161 cat("\tMAIN PROCESSING INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	162
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	163
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	164 #Verification of a group step before doing the fillpeaks job.
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	165
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	166 if (thefunction == "fillPeaks") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	167 res=try(is.null(groupnames(xset)))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	168 if (class(res) == "try-error"){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	169 error<-geterrmessage()
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	170 write(error, stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	171 stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	172 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	173
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	174 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	175
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	176 #change the default display settings
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	177 #dev.new(file="Rplots.pdf", width=16, height=12)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	178 pdf(file=rplotspdf, width=16, height=12)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	179 if (thefunction == "group") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	180 par(mfrow=c(2,2))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	181 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	182 #else if (thefunction == "retcor") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	183 #try to change the legend display
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	184 # par(xpd=NA)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	185 # par(xpd=T, mar=par()$mar+c(0,0,0,4))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	186 #}
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	187
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	188
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	189 #execution of the function "thefunction" with the parameters given in "listArguments"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	190 xset = do.call(thefunction, listArguments)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	191
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	192
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	193 cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	194
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	195 dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	196
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	197 if (thefunction == "xcmsSet") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	198
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	199 #transform the files absolute pathways into relative pathways
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	200 xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	201
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	202 if(exists("zipfile") && (zipfile!="")) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	203
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	204 #Modify the samples names (erase the path)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	205 for(i in 1:length(sampnames(xset))){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	206
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	207 sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	208 sample_name=sample_name[length(sample_name)]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	209 sample_name= unlist(strsplit(sample_name,"[.]"))[1]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	210 sampnames(xset)[i]=sample_name
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	211
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	212 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	213
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	214 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	215
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	216 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	217
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	218 # -- TIC --
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	219 if (thefunction == "xcmsSet") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	220 sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	221 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	222 getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	223 } else if (thefunction == "retcor") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	224 getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	225 getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	226 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	227
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	228 cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	229
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	230
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	231 # ----- EXPORT -----
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	232
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	233 cat("\tXSET OBJECT INFO\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	234 print(xset)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	235 #delete the parameters to avoid the passage to the next tool in .RData image
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	236
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	237
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	238 #saving R data in .Rdata file to save the variables used in the present tool
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	239 objects2save = c("xset","zipfile","listOFlistArguments","md5sumList","sampleNamesList")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	240 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	241
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	242 cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	243
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	244
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	245 cat("\tDONE\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: diff changeset	246

Mercurial > repos > lecorguille > xcms_retcor

annotate xcms.r @ 6:fcd93f47dcbf draft