Mercurial > repos > workflow4metabolomics > xcms_refine
changeset 3:6c2798bce3eb draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
| author | workflow4metabolomics |
|---|---|
| date | Mon, 03 Feb 2025 14:46:55 +0000 |
| parents | 090b33a9981c |
| children | |
| files | abims_xcms_refine.xml lib.r macros_xcms.xml xcms_refine.r |
| diffstat | 4 files changed, 391 insertions(+), 379 deletions(-) [+] |
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--- a/abims_xcms_refine.xml Mon Jul 15 16:00:52 2024 +0000 +++ b/abims_xcms_refine.xml Mon Feb 03 14:46:55 2025 +0000 @@ -8,11 +8,14 @@ </macros> <expand macro="requirements"/> - + <required_files> + <include path="xcms_refine.r" /> + <include path="lib.r" /> + </required_files> <expand macro="stdio"/> <command><![CDATA[ - @COMMAND_RSCRIPT@/xcms_refine.r + @COMMAND_RSCRIPT@xcms_refine.r image '$image' method $methods.method
--- a/lib.r Mon Jul 15 16:00:52 2024 +0000 +++ b/lib.r Mon Feb 03 14:46:55 2025 +0000 @@ -1,461 +1,470 @@ -#@authors ABiMS TEAM, Y. Guitton +# @authors ABiMS TEAM, Y. Guitton # lib.r for Galaxy Workflow4Metabolomics xcms tools -#@author G. Le Corguille +# @author G. Le Corguille # solve an issue with batch if arguments are logical TRUE/FALSE parseCommandArgs <- function(...) { - args <- batch::parseCommandArgs(...) - for (key in names(args)) { - if (args[key] %in% c("TRUE", "FALSE")) - args[key] <- as.logical(args[key]) - } - return(args) + args <- batch::parseCommandArgs(...) + for (key in names(args)) { + if (args[key] %in% c("TRUE", "FALSE")) { + args[key] <- as.logical(args[key]) + } + } + return(args) } -#@author G. Le Corguille +# @author G. Le Corguille # This function will # - load the packages # - display the sessionInfo loadAndDisplayPackages <- function(pkgs) { - for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE))) + for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE))) - sessioninfo <- sessionInfo() - cat(sessioninfo$R.version$version.string, "\n") - cat("Main packages:\n") - for (pkg in names(sessioninfo$otherPkgs)) { - cat(paste(pkg, packageVersion(pkg)), "\t") - } - cat("\n") - cat("Other loaded packages:\n") - for (pkg in names(sessioninfo$loadedOnly)) { - cat(paste(pkg, packageVersion(pkg)), "\t") - } - cat("\n") + sessioninfo <- sessionInfo() + cat(sessioninfo$R.version$version.string, "\n") + cat("Main packages:\n") + for (pkg in names(sessioninfo$otherPkgs)) { + cat(paste(pkg, packageVersion(pkg)), "\t") + } + cat("\n") + cat("Other loaded packages:\n") + for (pkg in names(sessioninfo$loadedOnly)) { + cat(paste(pkg, packageVersion(pkg)), "\t") + } + cat("\n") } -#@author G. Le Corguille +# @author G. Le Corguille # This function merge several chromBPI or chromTIC into one. mergeChrom <- function(chrom_merged, chrom) { - if (is.null(chrom_merged)) return(NULL) - chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) - return(chrom_merged) + if (is.null(chrom_merged)) { + return(NULL) + } + chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) + return(chrom_merged) } -#@author G. Le Corguille +# @author G. Le Corguille # This function merge several xdata into one. mergeXData <- function(args) { - chromTIC <- NULL - chromBPI <- NULL - chromTIC_adjusted <- NULL - chromBPI_adjusted <- NULL - md5sumList <- NULL - for (image in args$images) { + chromTIC <- NULL + chromBPI <- NULL + chromTIC_adjusted <- NULL + chromBPI_adjusted <- NULL + md5sumList <- NULL + for (image in args$images) { + load(image) + # Handle infiles + if (!exists("singlefile")) singlefile <- NULL + if (!exists("zipfile")) zipfile <- NULL + rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) + zipfile <- rawFilePath$zipfile + singlefile <- rawFilePath$singlefile - load(image) - # Handle infiles - if (!exists("singlefile")) singlefile <- NULL - if (!exists("zipfile")) zipfile <- NULL - rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) - zipfile <- rawFilePath$zipfile - singlefile <- rawFilePath$singlefile + if (exists("raw_data")) xdata <- raw_data + if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") - if (exists("raw_data")) xdata <- raw_data - if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") - - cat(sampleNamesList$sampleNamesOrigin, "\n") + cat(sampleNamesList$sampleNamesOrigin, "\n") - if (!exists("xdata_merged")) { - xdata_merged <- xdata - singlefile_merged <- singlefile - md5sumList_merged <- md5sumList - sampleNamesList_merged <- sampleNamesList - chromTIC_merged <- chromTIC - chromBPI_merged <- chromBPI - chromTIC_adjusted_merged <- chromTIC_adjusted - chromBPI_adjusted_merged <- chromBPI_adjusted - } else { - if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata) - else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata) - else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") + if (!exists("xdata_merged")) { + xdata_merged <- xdata + singlefile_merged <- singlefile + md5sumList_merged <- md5sumList + sampleNamesList_merged <- sampleNamesList + chromTIC_merged <- chromTIC + chromBPI_merged <- chromBPI + chromTIC_adjusted_merged <- chromTIC_adjusted + chromBPI_adjusted_merged <- chromBPI_adjusted + } else { + if (is(xdata, "XCMSnExp")) { + xdata_merged <- c(xdata_merged, xdata) + } else if (is(xdata, "OnDiskMSnExp")) { + xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata) + } else { + stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") + } - singlefile_merged <- c(singlefile_merged, singlefile) - md5sumList_merged$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) - chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) - chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) - chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) - chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) + 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$sampleNamesMakeNames) + chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) + chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) + chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) + chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) + } } - } - rm(image) - xdata <- xdata_merged - rm(xdata_merged) - singlefile <- singlefile_merged - rm(singlefile_merged) - md5sumList <- md5sumList_merged - rm(md5sumList_merged) - sampleNamesList <- sampleNamesList_merged - rm(sampleNamesList_merged) + rm(image) + xdata <- xdata_merged + rm(xdata_merged) + singlefile <- singlefile_merged + rm(singlefile_merged) + md5sumList <- md5sumList_merged + rm(md5sumList_merged) + sampleNamesList <- sampleNamesList_merged + rm(sampleNamesList_merged) - if (!is.null(args$sampleMetadata)) { - cat("\tXSET PHENODATA SETTING...\n") - sampleMetadataFile <- args$sampleMetadata - sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE) - xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)] + if (!is.null(args$sampleMetadata)) { + cat("\tXSET PHENODATA SETTING...\n") + sampleMetadataFile <- args$sampleMetadata + sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE) + xdata@phenoData@data$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 = " ")) - print(error_message) - stop(error_message) + 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 = " ")) + 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 +# @author G. Le Corguille # This function convert if it is required the Retention Time in minutes RTSecondToMinute <- function(variableMetadata, 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 - } - return(variableMetadata) + 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 + } + return(variableMetadata) } -#@author G. Le Corguille +# @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$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))]) - return(variableMetadata) + splitDeco <- strsplit(as.character(variableMetadata$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$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))]) + return(variableMetadata) } -#@author G. Le Corguille +# @author G. Le Corguille # This function convert the remain NA to 0 in the dataMatrix naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { - if (naTOzero) { - dataMatrix[is.na(dataMatrix)] <- 0 - } - return(dataMatrix) -} - -#@author G. Le Corguille -# Draw the plotChromPeakDensity 3 per page in a pdf file -getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) { - pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12) - - par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) - - if (length(unique(xdata$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 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 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() + if (naTOzero) { + dataMatrix[is.na(dataMatrix)] <- 0 + } + return(dataMatrix) } -#@author G. Le Corguille +# @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) + + par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) + + 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$sample_group) + for (i in seq_len(length(group_colors))) { + col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i] + } + + xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) + for (i in seq_len(nrow(featureDefinitions(xdata)))) { + mzmin <- featureDefinitions(xdata)[i, ]$mzmin + mzmax <- featureDefinitions(xdata)[i, ]$mzmax + plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit))) + legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) + } + + dev.off() +} + +# @author G. Le Corguille # Draw the plotChromPeakDensity 3 per page in a pdf file getPlotAdjustedRtime <- function(xdata) { - - pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12) + pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12) - # Color by group - if (length(unique(xdata$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) - } + # Color by group + 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$sample_group]) + legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) + } - # Color by sample - plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) - legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1) + # 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) - dev.off() + dev.off() } -#@author G. Le Corguille +# @author G. Le Corguille # value: intensity values to be used into, maxo or intb getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, 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) - variableMetadata <- featureDefinitions(xdata) - colnames(variableMetadata)[1] <- "mz" - colnames(variableMetadata)[4] <- "rt" - variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata) + dataMatrix <- featureValues(xdata, method = "medret", value = intval) + colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(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) - variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) - variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ) - dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) + variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) + 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 = ",") + # 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 = ",") - write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE) - write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE) - + write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE) + write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE) } -#@author G. Le Corguille +# @author G. Le Corguille # It allow different of field separators getDataFrameFromFile <- function(filename, header = TRUE) { - myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE) - if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE) - if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE) - if (ncol(myDataFrame) < 2) { - error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" - print(error_message) - stop(error_message) - } - return(myDataFrame) + myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE) + if (ncol(myDataFrame) < 2) { + error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" + print(error_message) + stop(error_message) + } + return(myDataFrame) } -#@author G. Le Corguille +# @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") { - - if (aggregationFun == "sum") - type <- "Total Ion Chromatograms" - else - type <- "Base Peak Intensity Chromatograms" + if (aggregationFun == "sum") { + type <- "Total Ion Chromatograms" + } else { + type <- "Base Peak Intensity Chromatograms" + } - adjusted <- "Raw" - if (hasAdjustedRtime(xdata)) - adjusted <- "Adjusted" + adjusted <- "Raw" + if (hasAdjustedRtime(xdata)) { + 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 - 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$sample_group) - plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none") - legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1) - } + # Color by group + 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[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) + # 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$sample_name)), cex = 0.8, lty = 1) - dev.off() + dev.off() } # Get the polarities from all the samples of a condition -#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +# @author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +# @author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") { - cat("Creating the sampleMetadata file...\n") + cat("Creating the sampleMetadata file...\n") - #Create the sampleMetada dataframe - sampleMetadata <- xdata@phenoData@data - rownames(sampleMetadata) <- NULL - colnames(sampleMetadata) <- c("sample_name", "class") + # Create the sampleMetada dataframe + sampleMetadata <- xdata@phenoData@data + rownames(sampleMetadata) <- NULL + colnames(sampleMetadata) <- c("sample_name", "class") - sampleNamesOrigin <- sampleMetadata$sample_name - sampleNamesMakeNames <- make.names(sampleNamesOrigin) + sampleNamesOrigin <- sampleMetadata$sample_name + sampleNamesMakeNames <- make.names(sampleNamesOrigin) - 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()) + 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()) + } + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") } - stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") - } - 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")) + 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")) + } } - } - sampleMetadata$sample_name <- sampleNamesMakeNames + sampleMetadata$sample_name <- sampleNamesMakeNames - #For each sample file, the following actions are done - for (fileIdx in seq_len(length(fileNames(xdata)))) { - #Check if the file is in the CDF format - if (!mzR:::netCDFIsFile(fileNames(xdata))) { - - # If the column isn't exist, with add one filled with NA - if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA + # For each sample file, the following actions are done + for (fileIdx in seq_len(length(fileNames(xdata)))) { + # Check if the file is in the CDF format + if (!mzR:::netCDFIsFile(fileNames(xdata))) { + # If the column isn't exist, with add one filled with NA + if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA - #Extract the polarity (a list of polarities) - polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"] - #Verify if all the scans have the same polarity - uniq_list <- unique(polarity) - if (length(uniq_list) > 1) { - polarity <- "mixed" - } else { - polarity <- as.character(uniq_list) - } + # Extract the polarity (a list of polarities) + polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"] + # Verify if all the scans have the same polarity + uniq_list <- unique(polarity) + if (length(uniq_list) > 1) { + polarity <- "mixed" + } else { + polarity <- as.character(uniq_list) + } - #Set the polarity attribute - sampleMetadata$polarity[fileIdx] <- polarity + # Set the polarity attribute + sampleMetadata$polarity[fileIdx] <- polarity + } } - } + 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 +# @author Gildas Le Corguille lecorguille@sb-roscoff.fr getMd5sum <- function(files) { - cat("Compute md5 checksum...\n") - library(tools) - return(as.matrix(md5sum(files))) + cat("Compute md5 checksum...\n") + library(tools) + return(as.matrix(md5sum(files))) } # 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 -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +# @author Gildas Le Corguille lecorguille@sb-roscoff.fr 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)]], "\\|")) + # 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)]], "\\|")) - 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] - # In case, an url is used to import data within Galaxy - singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1) - 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] + # In case, an url is used to import data within Galaxy + 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)]] + # zipfile - if the file are passed in the command arguments -> refresh zipfile + if (!is.null(args[[paste0("zipfile", prefix)]])) { + zipfile <- args[[paste0("zipfile", prefix)]] + } - # single - 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!") - print(error_message) - stop(error_message) - } + # single + 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!") + print(error_message) + stop(error_message) + } - if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE))) - file.copy(singlefile_galaxyPath, singlefile_sampleName) - files <- c(files, singlefile_sampleName) + if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE))) { + 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!") - print(error_message) - stop(error_message) - } - suppressWarnings(unzip(zipfile, unzip = "unzip")) + # 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!") + print(error_message) + stop(error_message) + } + suppressWarnings(unzip(zipfile, unzip = "unzip")) - #get the directory name - suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE)) - directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1]))) - directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] - directory <- "." - if (length(directories) == 1) directory <- directories + # get the directory name + suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE)) + directories <- unique(unlist(lapply(strsplit(filesInZip$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 = "|") - info <- file.info(directory) - 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)) + 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) + files <- c(directory[!info$isdir], listed) + exists <- file.exists(files) + files <- files[exists] + } + return(list(zipfile = zipfile, singlefile = singlefile, files = files)) } # This function retrieve a xset like object -#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +# @author Gildas Le Corguille lecorguille@sb-roscoff.fr getxcmsSetObject <- function(xobject) { - # XCMS 1.x - if (class(xobject) == "xcmsSet") - return(xobject) - # XCMS 3.x - if (class(xobject) == "XCMSnExp") { - # Get the legacy xcmsSet object - suppressWarnings(xset <- as(xobject, "xcmsSet")) - if (!is.null(xset@phenoData$sample_group)) - sampclass(xset) <- xset@phenoData$sample_group - else - sampclass(xset) <- "." - return(xset) - } + # XCMS 1.x + if (class(xobject) == "xcmsSet") { + return(xobject) + } + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, "xcmsSet")) + if (!is.null(xset@phenoData$sample_group)) { + sampclass(xset) <- xset@phenoData$sample_group + } else { + sampclass(xset) <- "." + } + return(xset) + } }
--- a/macros_xcms.xml Mon Jul 15 16:00:52 2024 +0000 +++ b/macros_xcms.xml Mon Feb 03 14:46:55 2025 +0000 @@ -2,7 +2,7 @@ <macros> <token name="@TOOL_VERSION@">3.12.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements>
--- a/xcms_refine.r Mon Jul 15 16:00:52 2024 +0000 +++ b/xcms_refine.r Mon Feb 03 14:46:55 2025 +0000 @@ -1,7 +1,7 @@ #!/usr/bin/env Rscript # ----- LOG FILE ----- -log_file <- file("log.txt", open = "wt") +log_file <- file("log.txt", open = "wt") sink(log_file) sink(log_file, type = "output") @@ -9,11 +9,11 @@ # ----- PACKAGE ----- cat("\tSESSION INFO\n") -#Import the different functions +# Import the different functions source_local <- function(fname) { - argv <- commandArgs(trailingOnly = FALSE) - base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) - source(paste(base_dir, fname, sep = "/")) + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep = "/")) } source_local("lib.r") @@ -32,23 +32,23 @@ # ----- PROCESSING INFILE ----- cat("\tARGUMENTS PROCESSING INFO\n") -#saving the specific parameters -args_method <- args$method -args_image <- args$image +# saving the specific parameters +args_method <- args$method +args_image <- args$image args_msLevel <- args$msLevel param_args <- list() if (args_method == "CleanPeaks") { - param_args$maxPeakwidth <- args$maxPeakwidth + param_args$maxPeakwidth <- args$maxPeakwidth } else if (args_method == "FilterIntensity") { - param_args$threshold <- args$threshold - param_args$value <- args$value - param_args$nValues <- args$nValues + param_args$threshold <- args$threshold + param_args$value <- args$value + param_args$nValues <- args$nValues } else if (args_method == "MergeNeighboringPeaks") { - param_args$expandRt <- args$expandRt - param_args$expandMz <- args$expandMz - param_args$ppm <- args$ppm - param_args$minProp <- args$minProp + param_args$expandRt <- args$expandRt + param_args$expandMz <- args$expandMz + param_args$ppm <- args$ppm + param_args$minProp <- args$minProp } cat("\n\n") @@ -57,7 +57,7 @@ # ----- ARGUMENTS PROCESSING ----- cat("\tINFILE PROCESSING INFO\n") -#image is an .RData file necessary to use xset variable given by previous tools +# image is an .RData file necessary to use xset variable given by previous tools load(args_image) if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*") @@ -78,20 +78,20 @@ cat("\t\tPREPARE PARAMETERS\n\n") if (args_method == "CleanPeaks") { - refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth) + refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth) } else if (args_method == "FilterIntensity") { - refineChromPeaksParam <- FilterIntensityParam( - threshold = param_args$threshold, - nValues = param_args$nValues, - value = param_args$value - ) + refineChromPeaksParam <- FilterIntensityParam( + threshold = param_args$threshold, + nValues = param_args$nValues, + value = param_args$value + ) } else if (args_method == "MergeNeighboringPeaks") { - refineChromPeaksParam <- MergeNeighboringPeaksParam( - expandRt = param_args$expandRt, - expandMz = param_args$expandMz, - ppm = param_args$ppm, - minProp = param_args$minProp - ) + refineChromPeaksParam <- MergeNeighboringPeaksParam( + expandRt = param_args$expandRt, + expandMz = param_args$expandMz, + ppm = param_args$ppm, + minProp = param_args$minProp + ) } cat(str(refineChromPeaksParam)) @@ -116,7 +116,7 @@ print(xset) cat("\n\n") -#saving R data in .Rdata file to save the variables used in the present tool +# saving R data in .Rdata file to save the variables used in the present tool objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")