Merge pull request #283 from workflow4metabolomics/pulsar-linting-fix

Pulsar linting fix
workflow4metabolomics · Jan 21, 2025 · d5cb3fe · d5cb3fe
2 parents 6551805 + 5a77047
commit d5cb3fe
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Showing 78 changed files with 8,154 additions and 40,504 deletions.
diff --git a/tools/camera/CAMERA_annotateDiffreport.r b/tools/camera/CAMERA_annotateDiffreport.r
@@ -5,9 +5,9 @@ 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 = "/"))
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
 }
 source_local("lib.r")
 
@@ -50,7 +50,7 @@ directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
 
 # Because so far CAMERA isn't compatible with the new XCMSnExp object
 if (exists("xdata")) {
-  xset <- getxcmsSetObject(xdata)
+    xset <- getxcmsSetObject(xdata)
 }
 
 cat("\n\n")

diff --git a/tools/camera/CAMERA_combinexsAnnos.r b/tools/camera/CAMERA_combinexsAnnos.r
@@ -3,11 +3,11 @@
 # ----- 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")
 
@@ -18,7 +18,7 @@ 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
+args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
 
 cat("\n\n")
@@ -27,7 +27,7 @@ cat("\n\n")
 # ----- PROCESSING INFILE -----
 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_pos)
 xaP <- xa
 
@@ -58,16 +58,16 @@ cat("\n\n")
 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$numDigitsRT,
-  variableMetadataOutput = "variableMetadata.tsv"
+    xaP = xaP, xaN = xaN,
+    diffrepP = diffrepP, diffrepN = diffrepN,
+    pos = args$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
+# 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")
 

diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
@@ -5,9 +5,9 @@ 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 = "/"))
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
 }
 source_local("lib.r")
 
@@ -27,34 +27,34 @@ print(args)
 
 # Function to convert "NULL" strings to actual NULL values
 convertNullString <- function(x) {
-  if (x == "NULL") {
-    return(NULL)
-  }
-  return(x)
+    if (x == "NULL") {
+        return(NULL)
+    }
+    return(x)
 }
 
 # Function to convert string to numeric lists
 convert_psg_list <- function(x) {
-  # Check if x is NULL or has zero length before further processing
-  if (is.null(x) || length(x) == 0) {
-    return(NULL)
-  }
-
-  # Force conversion to character
-  x <- as.character(x)
-
-  if (grepl("^[0-9]+$", x)) {
-    # If the string represents a single numeric value
-    return(as.numeric(x))
-  } else {
-    # Convert string representation of a list to a numeric vector
-    # Use a regular expression to split by common separators
-    return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
-  }
+    # Check if x is NULL or has zero length before further processing
+    if (is.null(x) || length(x) == 0) {
+        return(NULL)
+    }
+
+    # Force conversion to character
+    x <- as.character(x)
+
+    if (grepl("^[0-9]+$", x)) {
+        # If the string represents a single numeric value
+        return(as.numeric(x))
+    } else {
+        # Convert string representation of a list to a numeric vector
+        # Use a regular expression to split by common separators
+        return(as.numeric(unlist(strsplit(x, "[,;\\s]+"))))
+    }
 }
 
 for (arg in names(args)) {
-  args[[arg]] <- convertNullString(args[[arg]])
+    args[[arg]] <- convertNullString(args[[arg]])
 }
 
 # Convert only the 'psg_list' element in args
@@ -65,7 +65,7 @@ print(sapply(args, class))
 
 # Check if the image file exists
 if (!file.exists(args$image)) {
-  stop("The RData file does not exist: ", args$image)
+    stop("The RData file does not exist: ", args$image)
 }
 
 # ----- PROCESSING INFILE -----
@@ -88,41 +88,41 @@ args <- rawFilePath$args
 
 print(paste("singlefile :", singlefile))
 if (!is.null(singlefile)) {
-  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+    directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
 }
 
 # Check if the 'rules' argument in 'args' is NULL
 if (is.null(args$rules)) {
-  # If 'args$rules' is NULL, set 'rulset' to NULL
-  args$rulset <- NULL
+    # If 'args$rules' is NULL, set 'rulset' to NULL
+    args$rulset <- NULL
 } else {
-  # Try to read the rules file with different delimiters
-  delimiters <- c(";", "\t", ",") # List of possible delimiters
-  success <- FALSE # Flag to check if reading was successful
-
-  for (sep in delimiters) {
-    # Attempt to read the rules file with the current separator
-    args$rulset <- read.table(args$rules, header = TRUE, sep = sep)
-
-    # Check if the number of columns is at least 4
-    if (ncol(args$rulset) >= 4) {
-      success <- TRUE # Mark success if the format is correct
-      break # Exit the loop if the file was read successfully
+    # Try to read the rules file with different delimiters
+    delimiters <- c(";", "\t", ",") # List of possible delimiters
+    success <- FALSE # Flag to check if reading was successful
+
+    for (sep in delimiters) {
+        # Attempt to read the rules file with the current separator
+        args$rulset <- read.table(args$rules, header = TRUE, sep = sep)
+
+        # Check if the number of columns is at least 4
+        if (ncol(args$rulset) >= 4) {
+            success <- TRUE # Mark success if the format is correct
+            break # Exit the loop if the file was read successfully
+        }
+    }
+
+    # If reading the rules file failed for all delimiters
+    if (!success) {
+        # Display an error message if the file is not well formatted
+        error_message <- "The rules file appears to be improperly formatted. Accepted column separators are ;, tab, and ,."
+        print(error_message)
+        stop(error_message) # Stop execution with an error
     }
-  }
-
-  # If reading the rules file failed for all delimiters
-  if (!success) {
-    # Display an error message if the file is not well formatted
-    error_message <- "The rules file appears to be improperly formatted. Accepted column separators are ;, tab, and ,."
-    print(error_message)
-    stop(error_message) # Stop execution with an error
-  }
 }
 
 # Verify that the object xa is loaded
 if (!exists("xa")) {
-  stop("The object xa was not found in the RData file.")
+    stop("The object xa was not found in the RData file.")
 }
 
 print("Loaded xa object:")
@@ -139,26 +139,26 @@ print(xa)
 peakList <- getPeaklist(xa, intval = args$intval)
 
 if (length(phenoData@data$sample_name) == 1) {
-  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
-  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
-  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+    peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+    variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
 } else {
-  names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
-  names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
-
-  variableMetadata <- data.frame(
-    name = names_default,
-    name_custom = names_custom,
-    stringsAsFactors = FALSE
-  )
-  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+    names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
+    names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
+
+    variableMetadata <- data.frame(
+        name = names_default,
+        name_custom = names_custom,
+        stringsAsFactors = FALSE
+    )
+    variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
 }
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute && RTinMinute == FALSE) {
-  RTinMinute <- TRUE
-  variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
+    RTinMinute <- TRUE
+    variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
 }
 
 # Save the extracted peak list as a TSV file named 'variableMetadata.tsv'

diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
@@ -5,9 +5,9 @@ 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 = "/"))
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
 }
 source_local("lib.r")
 
@@ -30,7 +30,7 @@ print(sapply(args, class))
 
 # Check if the image file exists
 if (!file.exists(args$image)) {
-  stop("The RData file does not exist: ", args$image)
+    stop("The RData file does not exist: ", args$image)
 }
 
 # ----- PROCESSING INFILE -----
@@ -53,41 +53,41 @@ args <- rawFilePath$args
 
 print(paste("singlefile :", singlefile))
 if (!is.null(singlefile)) {
-  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+    directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
 }
 
 # Verify if the xa object is loaded
 if (!exists("xa")) {
-  stop("The xa object was not found in the RData file.")
+    stop("The xa object was not found in the RData file.")
 }
 
 print("xa object loaded:")
 print(xa)
 
 print("calcIsotopeMatrix")
 calcIsotopeMatrix <- function(maxiso = 4) {
-  if (!is.numeric(maxiso)) {
-    stop("Parameter maxiso is not numeric!\n")
-  } else if (maxiso < 1 || maxiso > 8) {
-    stop(paste(
-      "Parameter maxiso must be between 1 and 8. ",
-      "Otherwise, use your own IsotopeMatrix.\n"
-    ), sep = "")
-  }
-
-  isotopeMatrix <- matrix(NA, 8, 4)
-  colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax")
-
-  isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150)
-  isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200)
-  isotopeMatrix[3, ] <- c(1.000, 1.0040, 0.001, 200)
-  isotopeMatrix[4, ] <- c(1.000, 1.0040, 0.0001, 200)
-  isotopeMatrix[5, ] <- c(1.000, 1.0040, 0.00001, 200)
-  isotopeMatrix[6, ] <- c(1.000, 1.0040, 0.000001, 200)
-  isotopeMatrix[7, ] <- c(1.000, 1.0040, 0.0000001, 200)
-  isotopeMatrix[8, ] <- c(1.000, 1.0040, 0.00000001, 200)
-
-  return(isotopeMatrix[1:maxiso, , drop = FALSE])
+    if (!is.numeric(maxiso)) {
+        stop("Parameter maxiso is not numeric!\n")
+    } else if (maxiso < 1 || maxiso > 8) {
+        stop(paste(
+            "Parameter maxiso must be between 1 and 8. ",
+            "Otherwise, use your own IsotopeMatrix.\n"
+        ), sep = "")
+    }
+
+    isotopeMatrix <- matrix(NA, 8, 4)
+    colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax")
+
+    isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150)
+    isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200)
+    isotopeMatrix[3, ] <- c(1.000, 1.0040, 0.001, 200)
+    isotopeMatrix[4, ] <- c(1.000, 1.0040, 0.0001, 200)
+    isotopeMatrix[5, ] <- c(1.000, 1.0040, 0.00001, 200)
+    isotopeMatrix[6, ] <- c(1.000, 1.0040, 0.000001, 200)
+    isotopeMatrix[7, ] <- c(1.000, 1.0040, 0.0000001, 200)
+    isotopeMatrix[8, ] <- c(1.000, 1.0040, 0.00000001, 200)
+
+    return(isotopeMatrix[1:maxiso, , drop = FALSE])
 }
 
 isotopeMatrix <- calcIsotopeMatrix(args$maxiso)
@@ -103,26 +103,26 @@ print(xa)
 peakList <- getPeaklist(xa, intval = args$intval)
 
 if (length(phenoData@data$sample_name) == 1) {
-  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
-  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
-  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+    peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+    variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
 } else {
-  names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
-  names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
-
-  variableMetadata <- data.frame(
-    name = names_default,
-    name_custom = names_custom,
-    stringsAsFactors = FALSE
-  )
-  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+    names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
+    names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
+
+    variableMetadata <- data.frame(
+        name = names_default,
+        name_custom = names_custom,
+        stringsAsFactors = FALSE
+    )
+    variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
 }
 
 if (!exists("RTinMinute")) RTinMinute <- FALSE
 
 if (args$convertRTMinute && RTinMinute == FALSE) {
-  RTinMinute <- TRUE
-  variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
+    RTinMinute <- TRUE
+    variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
 }
 
 # Saves the extracted peak list as a TSV file named 'variableMetadata.tsv'