Mercurial > repos > workflow4metabolomics > camera_combinexsannos
changeset 4:04bf0efbe7f6 draft
"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
| author | workflow4metabolomics |
|---|---|
| date | Thu, 22 Apr 2021 10:26:47 +0000 |
| parents | c4264a101e28 |
| children | 6e177d24c565 |
| files | CAMERA_combinexsAnnos.r README.rst abims_CAMERA_combinexsAnnos.xml lib.r macros.xml repository_dependencies.xml |
| diffstat | 6 files changed, 202 insertions(+), 186 deletions(-) [+] |
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--- a/CAMERA_combinexsAnnos.r Mon Mar 30 13:16:38 2020 +0000 +++ b/CAMERA_combinexsAnnos.r Thu Apr 22 10:26:47 2021 +0000 @@ -4,18 +4,20 @@ cat("\tSESSION INFO\n") #Import the different functions -source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local <- function(fname) { + argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) +} source_local("lib.r") -pkgs=c("CAMERA","multtest","batch") +pkgs <- c("CAMERA", "multtest", "batch") loadAndDisplayPackages(pkgs) cat("\n\n"); # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") -args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -write.table(as.matrix(args), col.names=F, quote=F, sep='\t') +args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") cat("\n\n"); @@ -25,16 +27,16 @@ #image is an .RData file necessary to use xset variable given by previous tools load(args$image_pos) -xaP=xa +xaP <- xa -diffrepP=NULL -if (exists("diffrep")) diffrepP=diffrep +diffrepP <- NULL +if (exists("diffrep")) diffrepP <- diffrep load(args$image_neg) -xaN=xa +xaN <- xa -diffrepN=NULL -if (exists("diffrep")) diffrepN=diffrep +diffrepN <- NULL +if (exists("diffrep")) diffrepN <- diffrep cat("\n\n") @@ -44,8 +46,8 @@ cat("\tARGUMENTS PROCESSING INFO\n") # Save arguments to generate a report -if (!exists("listOFargs")) listOFargs=list() -listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args +if (!exists("listOFargs")) listOFargs <- list() +listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] <- args cat("\n\n") @@ -53,19 +55,19 @@ # ----- PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") -cAnnot=combinexsAnnos_function( - xaP=xaP,xaN=xaN, - diffrepP=diffrepP, diffrepN=diffrepN, - pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta, - convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT, - variableMetadataOutput="variableMetadata.tsv" +cAnnot <- combinexsAnnos_function( + xaP = xaP, xaN = xaN, + diffrepP = diffrepP, diffrepN = diffrepN, + pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta, + convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT, + variableMetadataOutput = "variableMetadata.tsv" ) # ----- EXPORT ----- #saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile") -save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData") +objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile") +save(list = objects2save[objects2save %in% ls()], file = "combinexsAnnos.RData") cat("\n\n")
--- a/README.rst Mon Mar 30 13:16:38 2020 +0000 +++ b/README.rst Thu Apr 22 10:26:47 2021 +0000 @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 2.2.6+camera1.46.0 - 12/04/2021** + +- UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_) + **Version 2.2.6+camera1.42.0** - 13/02/2020 UPGRADE: upgrade the CAMERA version from 1.38.1 to 1.42.0 (see CAMERA News_)
--- a/abims_CAMERA_combinexsAnnos.xml Mon Mar 30 13:16:38 2020 +0000 +++ b/abims_CAMERA_combinexsAnnos.xml Thu Apr 22 10:26:47 2021 +0000 @@ -211,6 +211,8 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS +@HELP_CAMERA_NEWVERSION_1460@ + @HELP_CAMERA_NEWVERSION_1420@ **Version 2.2.5 - 09/04/2019**
--- a/lib.r Mon Mar 30 13:16:38 2020 +0000 +++ b/lib.r Thu Apr 22 10:26:47 2021 +0000 @@ -5,8 +5,8 @@ parseCommandArgs <- function(...) { args <- batch::parseCommandArgs(...) for (key in names(args)) { - if (args[key] %in% c("TRUE","FALSE")) - args[key] = as.logical(args[key]) + if (args[key] %in% c("TRUE", "FALSE")) + args[key] <- as.logical(args[key]) } return(args) } @@ -16,14 +16,20 @@ # - load the packages # - display the sessionInfo loadAndDisplayPackages <- function(pkgs) { - for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE))) - sessioninfo = sessionInfo() - cat(sessioninfo$R.version$version.string,"\n") + sessioninfo <- sessionInfo() + cat(sessioninfo$R.version$version.string, "\n") cat("Main packages:\n") - for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + for (pkg in names(sessioninfo$otherPkgs)) { + cat(paste(pkg, packageVersion(pkg)), "\t") + } + cat("\n") cat("Other loaded packages:\n") - for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + for (pkg in names(sessioninfo$loadedOnly)) { + cat(paste(pkg, packageVersion(pkg)), "\t") + } + cat("\n") } # This function retrieve a xset like object @@ -31,18 +37,18 @@ getxcmsSetObject <- function(xobject) { # XCMS 1.x if (class(xobject) == "xcmsSet") - return (xobject) + return(xobject) # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object - suppressWarnings(xset <- as(xobject, 'xcmsSet')) + suppressWarnings(xset <- as(xobject, "xcmsSet")) if (is.null(xset@phenoData$sample_group)) - sampclass(xset) = "." + sampclass(xset) <- "." else sampclass(xset) <- xset@phenoData$sample_group if (!is.null(xset@phenoData$sample_name)) - rownames(xset@phenoData) = xset@phenoData$sample_name - return (xset) + rownames(xset@phenoData) <- xset@phenoData$sample_name + return(xset) } } @@ -51,138 +57,139 @@ diffreport_png2pdf <- function(filebase) { dir.create("pdf") - pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf") - pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf") + pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf") + pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf") - system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput)) - system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput)) + system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput)) + system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput)) } #@author G. Le Corguille #The function create a zip archive from the different png generated by diffreport diffreport_png2zip <- function() { - zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip")) - zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip")) + zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip")) + zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip")) } #The function create a zip archive from the different tabular generated by diffreport diffreport_tabular2zip <- function() { - zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip")) + zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip")) } #@author G. Le Corguille #This function convert if it is required the Retention Time in minutes RTSecondToMinute <- function(variableMetadata, convertRTMinute) { - if (convertRTMinute){ + if (convertRTMinute) { #converting the retention times (seconds) into minutes print("converting the retention times into minutes in the variableMetadata") - variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 - variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 - variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 + variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60 + variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60 + variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60 } - return (variableMetadata) + return(variableMetadata) } #@author G. Le Corguille #This function format ions identifiers -formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { - splitDeco = strsplit(as.character(variableMetadata$name),"_") - idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) - namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) - variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) +formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) { + splitDeco <- strsplit(as.character(variableMetadata$name), "_") + idsDeco <- sapply(splitDeco, function(x) { + deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco)) + }) + namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco)) + variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))]) return(variableMetadata) } #The function annotateDiffreport without the corr function which bugs -annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") { +annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") { # Resolve the bug with x11, with the function png - options(bitmapType='cairo') + options(bitmapType = "cairo") #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. - res=try(is.null(xset@filled)) + res <- try(is.null(xset@filled)) # ------ annot ------- - args$calcCiS=as.logical(args$calcCiS) - args$calcIso=as.logical(args$calcIso) - args$calcCaS=as.logical(args$calcCaS) + args$calcCiS <- as.logical(args$calcCiS) + args$calcIso <- as.logical(args$calcIso) + args$calcCaS <- as.logical(args$calcCaS) # common parameters - args4annotate = list(object=xset, - nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm, - maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac, - ppm=args$ppm,mzabs=args$mzabs,quick=args$quick, - polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval) + args4annotate <- list(object = xset, + nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm, + maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac, + ppm = args$ppm, mzabs = args$mzabs, quick = args$quick, + polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval) - # quick == FALSE - if(args$quick==FALSE) { - args4annotate = append(args4annotate, - list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval, - calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS)) + if (args$quick == FALSE) { + args4annotate <- append(args4annotate, + list(graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval, + calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS)) # no ruleset if (!is.null(args$multiplier)) { - args4annotate = append(args4annotate, - list(multiplier=args$multiplier)) + args4annotate <- append(args4annotate, + list(multiplier = args$multiplier)) } # ruleset else { - rulset=read.table(args$rules, h=T, sep=";") - if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t") - if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",") + rulset <- read.table(args$rules, h = T, sep = ";") + if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = "\t") + if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = ",") if (ncol(rulset) < 4) { - error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation" + error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation" print(error_message) stop(error_message) } - args4annotate = append(args4annotate, - list(rules=rulset)) + args4annotate <- append(args4annotate, + list(rules = rulset)) } } # launch annotate - xa = do.call("annotate", args4annotate) - peakList=getPeaklist(xa,intval=args$intval) - peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); + xa <- do.call("annotate", args4annotate) + peakList <- getPeaklist(xa, intval = args$intval) + peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name"); # --- Multi condition : diffreport --- - diffrepOri=NULL - if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) { + diffrepOri <- NULL + if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) >= 2) { #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. - res=try(is.null(xset@filled)) - classes=levels(sampclass(xset)) - x=1:(length(classes)-1) - for (i in seq(along=x) ) { - y=1:(length(classes)) - for (n in seq(along=y)){ - if(i+n <= length(classes)){ - filebase=paste(classes[i],class2=classes[i+n],sep="-vs-") + res <- try(is.null(xset@filled)) + classes <- levels(sampclass(xset)) + x <- 1:(length(classes) - 1) + for (i in seq(along = x)) { + y <- 1:(length(classes)) + for (n in seq(along = y)) { + if (i + n <= length(classes)) { + filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-") - diffrep=diffreport( - object=xset,class1=classes[i],class2=classes[i+n], - filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth, - sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0) + diffrep <- diffreport( + object = xset, class1 = classes[i], class2 = classes[i + n], + filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth, + sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0) - diffrepOri = diffrep + diffrepOri <- diffrep # renamming of the column rtmed to rt to fit with camera peaklist function output - colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt" - colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz" + colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt" + colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz" # combines results and reorder columns - diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) - diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))]) + diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F) + diffrep <- cbind(diffrep[, !(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))], diffrep[, (colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))]) - diffrep = RTSecondToMinute(diffrep, args$convertRTMinute) - diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) + diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute) + diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ) - if(args$sortpval){ - diffrep=diffrep[order(diffrep$pvalue), ] + if (args$sortpval) { + diffrep <- diffrep[order(diffrep$pvalue), ] } dir.create("tabular", showWarnings = FALSE) - write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) + write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = "")) if (args$eicmax != 0) { if (args$png2 == "pdf") @@ -198,28 +205,28 @@ } # --- variableMetadata --- - variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] - variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute) - variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) + variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] + variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute) + variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ) # if we have 2 conditions, we keep stat of diffrep - if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) { - variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) - if(exists("args[[\"sortpval\"]]")){ - variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] + if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) == 2) { + variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F) + if (exists("args[[\"sortpval\"]]")) { + variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ] } } - variableMetadataOri=variableMetadata - write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) + variableMetadataOri <- variableMetadata + write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput) - return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri)); + return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri)); } -combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL, - pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, - numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){ +combinexsAnnos_function <- function(xaP, xaN, diffrepP = NULL, diffrepN = NULL, + pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = F, numDigitsMZ = 0, + numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") { #Load the two Rdata to extract the xset objects from positive and negative mode cat("\tObject xset from positive mode\n") @@ -233,136 +240,131 @@ cat("\n") cat("\tCombining...\n") #Convert the string to numeric for creating matrix - row=as.numeric(strsplit(ruleset,",")[[1]][1]) - column=as.numeric(strsplit(ruleset,",")[[1]][2]) - ruleset=cbind(row,column) + row <- as.numeric(strsplit(ruleset, ",")[[1]][1]) + column <- as.numeric(strsplit(ruleset, ",")[[1]][2]) + ruleset <- cbind(row, column) #Test if the file comes from an older version tool if ((!is.null(xaP)) & (!is.null(xaN))) { #Launch the combinexsannos function from CAMERA - cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset) + cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset) } else { stop("You must relauch the CAMERA.annotate step with the lastest version.") } - if(pos){ - xa=xaP - mode="neg. Mode" + if (pos) { + xa <- xaP + mode <- "neg. Mode" } else { - xa=xaN - mode="pos. Mode" + xa <- xaN + mode <- "pos. Mode" } - peakList=getPeaklist(xa) - peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); - variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]); - variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] + peakList <- getPeaklist(xa) + peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name"); + variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)]); + variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] #Test if there are more than two classes (conditions) - if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { - diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="") - diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="") + if (nlevels(sampclass(xaP@xcmsSet)) == 2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { + diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "") + diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "") - variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name") - variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name") + variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name") + variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name") } - rownames(variableMetadata) = NULL - #TODO: checker - #colnames(variableMetadata)[1:2] = c("name","mz/rt"); + rownames(variableMetadata) <- NULL + #TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt"); - variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute) - variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) + variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) + variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ) #If the user want to keep only the metabolites which match a difference - if(keep_meta){ - variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",] + if (keep_meta) { + variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ] } #Write the output into a tsv file - write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) + write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput) return(variableMetadata); } # This function get the raw file path from the arguments getRawfilePathFromArguments <- function(singlefile, zipfile, args) { - if (!is.null(args$zipfile)) zipfile = args$zipfile - if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive - if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative + if (!is.null(args$zipfile)) zipfile <- args$zipfile + if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive + if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative if (!is.null(args$singlefile_galaxyPath)) { - singlefile_galaxyPaths = args$singlefile_galaxyPath; - singlefile_sampleNames = args$singlefile_sampleName + singlefile_galaxyPaths <- args$singlefile_galaxyPath; + singlefile_sampleNames <- args$singlefile_sampleName } if (!is.null(args$singlefile_galaxyPathPositive)) { - singlefile_galaxyPaths = args$singlefile_galaxyPathPositive; - singlefile_sampleNames = args$singlefile_sampleNamePositive + singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive; + singlefile_sampleNames <- args$singlefile_sampleNamePositive } if (!is.null(args$singlefile_galaxyPathNegative)) { - singlefile_galaxyPaths = args$singlefile_galaxyPathNegative; - singlefile_sampleNames = args$singlefile_sampleNameNegative + singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative; + singlefile_sampleNames <- args$singlefile_sampleNameNegative } - if (exists("singlefile_galaxyPaths")){ - singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) - singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) + if (exists("singlefile_galaxyPaths")) { + singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ",")) + singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ",")) - singlefile=NULL - for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { - singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] - singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] - singlefile[[singlefile_sampleName]] = singlefile_galaxyPath + singlefile <- NULL + for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) { + singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] + singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath } } for (argument in c("zipfile", "zipfilePositive", "zipfileNegative", "singlefile_galaxyPath", "singlefile_sampleName", "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive", - "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { - args[[argument]]=NULL + "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative")) { + args[[argument]] <- NULL } - return(list(zipfile=zipfile, singlefile=singlefile, args=args)) + return(list(zipfile = zipfile, singlefile = singlefile, args = args)) } # This function retrieve the raw file in the working directory # - if zipfile: unzip the file with its directory tree # - if singlefiles: set symlink with the good filename -retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { - if(!is.null(singlefile) && (length("singlefile")>0)) { +retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) { + if (!is.null(singlefile) && (length("singlefile") > 0)) { for (singlefile_sampleName in names(singlefile)) { - singlefile_galaxyPath = singlefile[[singlefile_sampleName]] - if(!file.exists(singlefile_galaxyPath)){ - error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] + if (!file.exists(singlefile_galaxyPath)) { + error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!") print(error_message); stop(error_message) } - file.symlink(singlefile_galaxyPath,singlefile_sampleName) + file.symlink(singlefile_galaxyPath, singlefile_sampleName) } - directory = "." + directory <- "." } - if(!is.null(zipfile) && (zipfile!="")) { - if(!file.exists(zipfile)){ - error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + if (!is.null(zipfile) && (zipfile != "")) { + if (!file.exists(zipfile)) { + error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!") print(error_message) stop(error_message) } - #list all file in the zip file - #zip_files=unzip(zipfile,list=T)[,"Name"] - #unzip - suppressWarnings(unzip(zipfile, unzip="unzip")) + suppressWarnings(unzip(zipfile, unzip = "unzip")) #get the directory name - filesInZip=unzip(zipfile, list=T); - directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); - directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] - directory = "." - if (length(directories) == 1) directory = directories + filesInZip <- unzip(zipfile, list = T); + directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1]))); + directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory <- "." + if (length(directories) == 1) directory <- directories - cat("files_root_directory\t",directory,"\n") + cat("files_root_directory\t", directory, "\n") } - return (directory) + return(directory) } -
--- a/macros.xml Mon Mar 30 13:16:38 2020 +0000 +++ b/macros.xml Thu Apr 22 10:26:47 2021 +0000 @@ -1,14 +1,14 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.42.0</token> + <token name="@TOOL_VERSION@">1.46.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="0.4_3">r-snow</requirement> <requirement type="package" version="@TOOL_VERSION@">bioconductor-camera</requirement> - <requirement type="package" version="2.42.0">bioconductor-multtest</requirement> + <requirement type="package" version="2.46.0">bioconductor-multtest</requirement> <requirement type="package" version="1.1_5">r-batch</requirement> - <requirement type="package" version="1.3.31">graphicsmagick</requirement> + <requirement type="package" version="1.3.35">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio"> @@ -160,6 +160,12 @@ </token> + <token name="@HELP_CAMERA_NEWVERSION_1460@"> +**Version 2.2.6+camera1.46.0 - 12/04/2021** + +- UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_) + </token> + <token name="@HELP_CAMERA_NEWVERSION_1420@"> **Version 2.2.6+camera1.42.0 - 13/02/2020**
--- a/repository_dependencies.xml Mon Mar 30 13:16:38 2020 +0000 +++ b/repository_dependencies.xml Thu Apr 22 10:26:47 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="eb0248b80680" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> - <repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> + <repository name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="eb0248b80680"/> + <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="8ce71291b600"/> </repositories> \ No newline at end of file