Mercurial > repos > lecorguille > xcms_xcmsset
changeset 32:b02d1992a43a draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
| author | workflow4metabolomics |
|---|---|
| date | Wed, 07 Apr 2021 16:47:14 +0000 |
| parents | eb15a3841da4 |
| children | f5d51091cf84 |
| files | README.rst abims_xcms_xcmsSet.xml lib.r macros_xcms.xml repository_dependencies.xml test-data/faahKO.raw.RData test-data/faahKO_reduce.zip xcms_xcmsSet.r |
| diffstat | 8 files changed, 180 insertions(+), 140 deletions(-) [+] |
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--- a/README.rst Tue Apr 28 09:35:10 2020 -0400 +++ b/README.rst Wed Apr 07 16:47:14 2021 +0000 @@ -24,6 +24,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +**Version 3.12.0+galaxy* - 03/03/2020** + +- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) + **Version 3.6.1.0 - 03/09/2019** - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
--- a/abims_xcms_xcmsSet.xml Tue Apr 28 09:35:10 2020 -0400 +++ b/abims_xcms_xcmsSet.xml Wed Apr 07 16:47:14 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy1"> +<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> <description>Chromatographic peak detection</description> <macros> @@ -500,11 +500,11 @@ Changelog/News -------------- -.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS +@HELP_XCMS_NEWVERSION_31200@ **Version 3.6.1+galaxy1 - 22/04/2020** -- NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods. +- NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods. @HELP_XCMS_NEWVERSION_3610@
--- a/lib.r Tue Apr 28 09:35:10 2020 -0400 +++ b/lib.r Wed Apr 07 16:47:14 2021 +0000 @@ -6,8 +6,8 @@ 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) } @@ -17,14 +17,20 @@ # - 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") } #@author G. Le Corguille @@ -43,20 +49,20 @@ chromTIC_adjusted <- NULL chromBPI_adjusted <- NULL md5sumList <- NULL - for(image in args$images) { + for (image in args$images) { load(image) # Handle infiles if (!exists("singlefile")) singlefile <- NULL if (!exists("zipfile")) zipfile <- NULL - rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) + rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile if (exists("raw_data")) xdata <- raw_data if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") - cat(sampleNamesList$sampleNamesOrigin,"\n") + cat(sampleNamesList$sampleNamesOrigin, "\n") if (!exists("xdata_merged")) { xdata_merged <- xdata @@ -68,14 +74,14 @@ chromTIC_adjusted_merged <- chromTIC_adjusted chromBPI_adjusted_merged <- chromBPI_adjusted } else { - if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) - else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) + if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata) + else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata) else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") - singlefile_merged <- c(singlefile_merged,singlefile) - md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) - sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) - sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) + singlefile_merged <- c(singlefile_merged, singlefile) + md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin) + sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin) + sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames) chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) @@ -91,75 +97,93 @@ if (!is.null(args$sampleMetadata)) { cat("\tXSET PHENODATA SETTING...\n") sampleMetadataFile <- args$sampleMetadata - sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) - xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] + sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = F) + xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)] if (any(is.na(pData(xdata)$sample_group))) { sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] - error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) + error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " ")) print(error_message) stop(error_message) } } - if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } - if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } - if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } - if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } + if (!is.null(chromTIC_merged)) { + chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData + } + if (!is.null(chromBPI_merged)) { + chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData + } + if (!is.null(chromTIC_adjusted_merged)) { + chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData + } + if (!is.null(chromBPI_adjusted_merged)) { + chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData + } - return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) + return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted)) } #@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$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))]) return(variableMetadata) } #@author G. Le Corguille # This function convert the remain NA to 0 in the dataMatrix naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { - if (naTOzero){ + if (naTOzero) { dataMatrix[is.na(dataMatrix)] <- 0 } - return (dataMatrix) + return(dataMatrix) } #@author G. Le Corguille # Draw the plotChromPeakDensity 3 per page in a pdf file -getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) { - pdf(file="plotChromPeakDensity.pdf", width=16, height=12) +getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) { + pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12) par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) - group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + if (length(unique(xdata$sample_group)) < 10) { + group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + }else{ + group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3") + } names(group_colors) <- unique(xdata$sample_group) col_per_samp <- as.character(xdata$sample_group) - for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]} + for (i in seq_len(length(group_colors))) { + col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i] + } xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) - for (i in 1:nrow(featureDefinitions(xdata))) { - mzmin = featureDefinitions(xdata)[i,]$mzmin - mzmax = featureDefinitions(xdata)[i,]$mzmax - plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) - legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + for (i in seq_len(nrow(featureDefinitions(xdata)))) { + mzmin <- featureDefinitions(xdata)[i, ]$mzmin + mzmax <- featureDefinitions(xdata)[i, ]$mzmax + plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit))) + legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) } dev.off() @@ -169,53 +193,57 @@ # Draw the plotChromPeakDensity 3 per page in a pdf file getPlotAdjustedRtime <- function(xdata) { - pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) + pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12) # Color by group - group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + if (length(unique(xdata$sample_group)) < 10) { + group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + } else { + group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3") + } if (length(group_colors) > 1) { names(group_colors) <- unique(xdata$sample_group) plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) - legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) } # Color by sample plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) - legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) + legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1) dev.off() } #@author G. Le Corguille # value: intensity values to be used into, maxo or intb -getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { - dataMatrix <- featureValues(xdata, method="medret", value=intval) +getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = F, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { + dataMatrix <- featureValues(xdata, method = "medret", value = intval) colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) - dataMatrix = cbind(name=groupnames(xdata), dataMatrix) + dataMatrix <- cbind(name = groupnames(xdata), dataMatrix) variableMetadata <- featureDefinitions(xdata) - colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" - variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) + colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt" + variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata) variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) - variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) + variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ) dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) # FIX: issue when the vector at peakidx is too long and is written in a new line during the export - variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") + variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") - write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) - write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) + write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = F, row.names = F) + write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = F, row.names = F) } #@author G. Le Corguille # It allow different of field separators -getDataFrameFromFile <- function(filename, header=T) { - myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) - if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) - if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) +getDataFrameFromFile <- function(filename, header = T) { + myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = F) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = F) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = F) if (ncol(myDataFrame) < 2) { - error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" + error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" print(error_message) stop(error_message) } @@ -225,32 +253,36 @@ #@author G. Le Corguille # Draw the BPI and TIC graphics # colored by sample names or class names -getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { +getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") { if (aggregationFun == "sum") - type="Total Ion Chromatograms" + type <- "Total Ion Chromatograms" else - type="Base Peak Intensity Chromatograms" + type <- "Base Peak Intensity Chromatograms" - adjusted="Raw" + adjusted <- "Raw" if (hasAdjustedRtime(xdata)) - adjusted="Adjusted" + adjusted <- "Adjusted" - main <- paste(type,":",adjusted,"data") + main <- paste(type, ":", adjusted, "data") - pdf(pdfname, width=16, height=10) + pdf(pdfname, width = 16, height = 10) # Color by group - group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + if (length(unique(xdata$sample_group)) < 10) { + group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") + }else{ + group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3") + } if (length(group_colors) > 1) { names(group_colors) <- unique(xdata$sample_group) - plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none") - legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none") + legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) } # Color by sample - plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none") - legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) + plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none") + legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1) dev.off() } @@ -259,7 +291,7 @@ # Get the polarities from all the samples of a condition #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM -getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { +getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") { cat("Creating the sampleMetadata file...\n") #Create the sampleMetada dataframe @@ -273,7 +305,7 @@ if (any(duplicated(sampleNamesMakeNames))) { write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) for (sampleName in sampleNamesOrigin) { - write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) + write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr()) } stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") } @@ -281,7 +313,7 @@ if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") for (sampleName in sampleNamesOrigin) { - cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) + cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n")) } } @@ -289,7 +321,7 @@ #For each sample file, the following actions are done - for (fileIdx in 1:length(fileNames(xdata))) { + for (fileIdx in seq_len(length(fileNames(xdata)))) { #Check if the file is in the CDF format if (!mzR:::netCDFIsFile(fileNames(xdata))) { @@ -297,10 +329,10 @@ if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA #Extract the polarity (a list of polarities) - polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] + polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"] #Verify if all the scans have the same polarity uniq_list <- unique(polarity) - if (length(uniq_list)>1){ + if (length(uniq_list) > 1) { polarity <- "mixed" } else { polarity <- as.character(uniq_list) @@ -312,16 +344,16 @@ } - write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) + write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput) - return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) + return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames)) } # This function will compute MD5 checksum to check the data integrity #@author Gildas Le Corguille lecorguille@sb-roscoff.fr -getMd5sum <- function (files) { +getMd5sum <- function(files) { cat("Compute md5 checksum...\n") library(tools) return(as.matrix(md5sum(files))) @@ -331,71 +363,71 @@ # - if zipfile: unzip the file with its directory tree # - if singlefiles: set symlink with the good filename #@author Gildas Le Corguille lecorguille@sb-roscoff.fr -retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") { +retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") { - if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") + if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") # single - if the file are passed in the command arguments -> refresh singlefile - if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { - singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|")) - singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|")) + if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) { + singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|")) + singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|")) singlefile <- NULL - for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { + for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) { singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] # In case, an url is used to import data within Galaxy - singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) + singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1) singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath } } # zipfile - if the file are passed in the command arguments -> refresh zipfile - if (!is.null(args[[paste0("zipfile",prefix)]])) - zipfile <- args[[paste0("zipfile",prefix)]] + if (!is.null(args[[paste0("zipfile", prefix)]])) + zipfile <- args[[paste0("zipfile", prefix)]] # single - if(!is.null(singlefile) && (length("singlefile")>0)) { + if (!is.null(singlefile) && (length("singlefile") > 0)) { files <- vector() 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!") + 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) } - if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) + if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T))) file.copy(singlefile_galaxyPath, singlefile_sampleName) files <- c(files, singlefile_sampleName) } } # zipfile - 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) } - suppressWarnings(unzip(zipfile, unzip="unzip")) + suppressWarnings(unzip(zipfile, unzip = "unzip")) #get the directory name - suppressWarnings(filesInZip <- unzip(zipfile, list=T)) - directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) + suppressWarnings(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") - filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") - filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|") info <- file.info(directory) - listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) + listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE) files <- c(directory[!info$isdir], listed) exists <- file.exists(files) files <- files[exists] } - return(list(zipfile=zipfile, singlefile=singlefile, files=files)) + return(list(zipfile = zipfile, singlefile = singlefile, files = files)) } @@ -405,15 +437,15 @@ getxcmsSetObject <- function(xobject) { # XCMS 1.x if (class(xobject) == "xcmsSet") - return (xobject) + return(xobject) # XCMS 3.x if (class(xobject) == "XCMSnExp") { # Get the legacy xcmsSet object - suppressWarnings(xset <- as(xobject, 'xcmsSet')) + suppressWarnings(xset <- as(xobject, "xcmsSet")) if (!is.null(xset@phenoData$sample_group)) sampclass(xset) <- xset@phenoData$sample_group else sampclass(xset) <- "." - return (xset) + return(xset) } }
--- a/macros_xcms.xml Tue Apr 28 09:35:10 2020 -0400 +++ b/macros_xcms.xml Wed Apr 07 16:47:14 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.6.1</token> + <token name="@TOOL_VERSION@">3.12.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> @@ -243,6 +243,7 @@ .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html +.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS </token> @@ -256,6 +257,11 @@ - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) </token> + <token name="@HELP_XCMS_NEWVERSION_31200@"> +**Version 3.12.0+galaxy* - 03/03/2020** + +- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) + </token> <xml name="citation"> <citations>
--- a/repository_dependencies.xml Tue Apr 28 09:35:10 2020 -0400 +++ b/repository_dependencies.xml Wed Apr 07 16:47:14 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> - <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="7800ba9a4c1e"/> + <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/> </repositories> \ No newline at end of file
--- a/xcms_xcmsSet.r Tue Apr 28 09:35:10 2020 -0400 +++ b/xcms_xcmsSet.r Wed Apr 07 16:47:14 2021 +0000 @@ -1,7 +1,7 @@ #!/usr/bin/env Rscript # ----- LOG FILE ----- -log_file <- file("log.txt", open="wt") +log_file <- file("log.txt", open = "wt") sink(log_file) sink(log_file, type = "output") @@ -10,10 +10,12 @@ 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("xcms","batch") +pkgs <- c("xcms", "batch") loadAndDisplayPackages(pkgs) cat("\n\n"); @@ -21,7 +23,7 @@ # ----- 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') +write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") cat("\n\n") @@ -31,7 +33,7 @@ #saving the commun parameters BPPARAM <- MulticoreParam(1) -if (!is.null(args$BPPARAM)){ +if (!is.null(args$BPPARAM)) { BPPARAM <- MulticoreParam(args$BPPARAM) } register(BPPARAM) @@ -44,7 +46,7 @@ method <- args$method -if (!is.null(args$roiList)){ +if (!is.null(args$roiList)) { cat("\t\troiList provided\n") args$roiList <- list(getDataFrameFromFile(args$roiList)) print(args$roiList) @@ -60,7 +62,7 @@ if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData") # Handle infiles -rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) +rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile @@ -79,34 +81,30 @@ if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) #Apply this filter only if file contain MS and MSn -if(length(unique(msLevel(raw_data)))!= 1){ - raw_data <- filterMsLevel(raw_data,msLevel=1) +if (length(unique(msLevel(raw_data))) != 1) { + raw_data <- filterMsLevel(raw_data, msLevel = 1) } cat("\t\t\tChromatographic peak detection\n") # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... -args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] +args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] -findChromPeaksParam <- do.call(paste0(method,"Param"), args) +findChromPeaksParam <- do.call(paste0(method, "Param"), args) print(findChromPeaksParam) -xdata <- findChromPeaks(raw_data, param=findChromPeaksParam) +xdata <- findChromPeaks(raw_data, param = findChromPeaksParam) # Check if there are no peaks if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings") # Create a sampleMetada file -sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv") - -#cat("\t\t\tCompute and Store TIC and BPI\n") -#chromTIC = chromatogram(xdata, aggregationFun = "sum") -#chromBPI = chromatogram(xdata, aggregationFun = "max") +sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv") # Create a chromPeaks table if required if (exists("peaklistParam")) { - if(peaklistParam){ - cat("\nCreating the chromatographic peaks' table...\n") - write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F) - } + if (peaklistParam) { + cat("\nCreating the chromatographic peaks' table...\n") + write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = F, row.names = F) + } } cat("\n\n") @@ -124,8 +122,8 @@ cat("\n\n") #saving R data in .Rdata file to save the variables used in the present tool -objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") -save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData") +objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") +save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData") cat("\tDONE\n")