Add "singlefile_galaxyPath" and "singlefile_sampleName" arguments

tools/camera/CAMERA_findAdducts.R

@@ -10,46 +10,40 @@ args_vec <- commandArgs(trailingOnly = TRUE)
 print("Arguments retrieved from the command line:")
 print(args_vec)
 
-# # Function to convert "NULL" strings to actual NULL values
-# convertNullString <- function(x) {
-#   if (x == "NULL") {
-#     return(NULL)
-#   }
-#   return(x)
-# }
-
 args <- list(
-  image           = args_vec[1], # the xsAnnotate object
-  ppm             = as.numeric(args_vec[2]), # ppm error for the search
-  mzabs           = as.numeric(args_vec[3]), # allowed variance for the search
-  multiplier      = as.numeric(args_vec[4]), # highest number(n) of allowed clusterion [nM+ion]
-  polarity        = args_vec[5], # Which polarity mode was used for measuring of the MS sample
-  rules           = args_vec[6], # custom ruleset or NULL for default ruleset
-  max_peaks       = as.numeric(args_vec[7]), # If run in parallel mode, this number defines how many peaks will be calculated in each thread
-  psg_list        = args_vec[8], # Vector of pseudospectra indices; correlation analysis will only be done for those groups
-  intval          = args_vec[9], # choose intensity values. Allowed values are "into", "maxo", "intb" (string)
+  image = args_vec[1], # the xsAnnotate object
+  ppm = as.numeric(args_vec[2]), # ppm error for the search
+  mzabs = as.numeric(args_vec[3]), # allowed variance for the search
+  multiplier = as.numeric(args_vec[4]), # highest number(n) of allowed clusterion [nM+ion]
+  polarity = args_vec[5], # Which polarity mode was used for measuring of the MS sample
+  rules = args_vec[6], # custom ruleset or NULL for default ruleset
+  max_peaks = as.numeric(args_vec[7]), # If run in parallel mode, this number defines how many peaks will be calculated in each thread
+  psg_list = args_vec[8], # Vector of pseudospectra indices; correlation analysis will only be done for those groups
+  intval = args_vec[9], # choose intensity values. Allowed values are "into", "maxo", "intb" (string)
   convertRTMinute = as.logical(args_vec[10]), # TRUE - FALSE
-  numDigitsMZ     = as.numeric(args_vec[11]), # Number of digits MZ
-  numDigitsRT     = as.numeric(args_vec[12]) # Number of digits RT
+  numDigitsMZ = as.numeric(args_vec[11]), # Number of digits MZ
+  numDigitsRT = as.numeric(args_vec[12]), # Number of digits RT
+  singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[14] # @COMMAND_FILE_LOAD@
 )
 
 # Check if the 'rules' argument in 'args' is NULL
 if (is.null(args$rules)) {
   # If 'args$rules' is NULL, set 'rulset' to NULL
-  args$rulset <- NULL 
+  args$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
+  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
+      success <- TRUE # Mark success if the format is correct
+      break # Exit the loop if the file was read successfully
     }
   }
 
@@ -58,7 +52,7 @@ if (is.null(args$rules)) {
     # 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
+    stop(error_message) # Stop execution with an error
   }
 }
 

tools/camera/CAMERA_findIsotopes.R

@@ -11,17 +11,19 @@ print("Arguments retrieved from command line:")
 print(args_vec)
 
 args <- list(
-  image           = args_vec[1], # the xsAnnotate object
-  maxcharge       = as.numeric(args_vec[2]), # max. number of the isotope charge
-  maxiso          = as.numeric(args_vec[3]), # max. number of the isotope peaks
-  ppm             = as.numeric(args_vec[4]), # ppm error for the search
-  mzabs           = as.numeric(args_vec[5]), # allowed variance for the search
-  intval          = args_vec[6], # Intensity parameter ("into", "maxo", "intb")
-  minfrac         = as.numeric(args_vec[7]), # In case of multiple samples, percentage value of samples, which must contain the correct C12/C13 ratio and are not NA
-  filter          = as.logical(args_vec[8]), # Should C12/C13 filter be applied?
+  image = args_vec[1], # the xsAnnotate object
+  maxcharge = as.numeric(args_vec[2]), # max. number of the isotope charge
+  maxiso = as.numeric(args_vec[3]), # max. number of the isotope peaks
+  ppm = as.numeric(args_vec[4]), # ppm error for the search
+  mzabs = as.numeric(args_vec[5]), # allowed variance for the search
+  intval = args_vec[6], # Intensity parameter ("into", "maxo", "intb")
+  minfrac = as.numeric(args_vec[7]), # In case of multiple samples, percentage value of samples, which must contain the correct C12/C13 ratio and are not NA
+  filter = as.logical(args_vec[8]), # Should C12/C13 filter be applied?
   convertRTMinute = as.logical(args_vec[9]), # TRUE - FALSE
-  numDigitsMZ     = as.numeric(args_vec[10]), # Number of digits MZ
-  numDigitsRT     = as.numeric(args_vec[11]) # Number of digits RT
+  numDigitsMZ = as.numeric(args_vec[10]), # Number of digits MZ
+  numDigitsRT = as.numeric(args_vec[11]), # Number of digits RT
+  singlefile_galaxyPath = args_vec[12], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[13] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")

tools/camera/CAMERA_groupCorr.R

@@ -11,18 +11,20 @@ print("Command-line arguments retrieved:")
 print(args_vec)
 
 args <- list(
-  image           = args_vec[1], # the xsAnnotate object
-  cor_eic_th      = as.numeric(args_vec[2]), # Correlation threshold for EIC correlation
-  pval            = as.numeric(args_vec[3]), # p-value threshold for testing correlation significance
-  graphMethod     = args_vec[4], # Clustering method for resulting correlation graph. See calcPC for more details.
-  calcIso         = as.logical(args_vec[5]), # Include isotope detection information for graph clustering
-  calcCiS         = as.logical(args_vec[6]), # Calculate correlation inside samples
-  calcCaS         = as.logical(args_vec[7]), # Calculate correlation across samples
-  cor_exp_th      = as.numeric(args_vec[8]), # Threshold for intensity correlations across samples
-  intval          = args_vec[9], # Selection of the intensity values (such as "into") used in the correlation analysis. See getPeaklist for all allowed values.
-  numDigitsMZ     = as.numeric(args_vec[10]), # Digits for MZ "customname"
-  numDigitsRT     = as.numeric(args_vec[11]), # Digits for RT "customname"
-  convertRTMinute = as.logical(args_vec[12]) # TRUE - FALSE
+  image = args_vec[1], # the xsAnnotate object
+  cor_eic_th = as.numeric(args_vec[2]), # Correlation threshold for EIC correlation
+  pval = as.numeric(args_vec[3]), # p-value threshold for testing correlation significance
+  graphMethod = args_vec[4], # Clustering method for resulting correlation graph. See calcPC for more details.
+  calcIso = as.logical(args_vec[5]), # Include isotope detection information for graph clustering
+  calcCiS = as.logical(args_vec[6]), # Calculate correlation inside samples
+  calcCaS = as.logical(args_vec[7]), # Calculate correlation across samples
+  cor_exp_th = as.numeric(args_vec[8]), # Threshold for intensity correlations across samples
+  intval = args_vec[9], # Selection of the intensity values (such as "into") used in the correlation analysis. See getPeaklist for all allowed values.
+  numDigitsMZ = as.numeric(args_vec[10]), # Digits for MZ "customname"
+  numDigitsRT = as.numeric(args_vec[11]), # Digits for RT "customname"
+  convertRTMinute = as.logical(args_vec[12]), # TRUE - FALSE
+  singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[14] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")

tools/camera/CAMERA_groupFWHM.R

@@ -12,13 +12,15 @@ print(args_vec)
 
 # Convert arguments to appropriate types
 args <- list(
-  image           = args_vec[1], # RData input file
-  sigma           = as.numeric(args_vec[2]), # Convert sigma to numeric
-  perfwhm         = as.numeric(args_vec[3]), # Convert perfwhm to numeric
-  intval          = args_vec[4], # intval parameter ("into", "maxo", "intb")
+  image = args_vec[1], # RData input file
+  sigma = as.numeric(args_vec[2]), # Convert sigma to numeric
+  perfwhm = as.numeric(args_vec[3]), # Convert perfwhm to numeric
+  intval = args_vec[4], # intval parameter ("into", "maxo", "intb")
   convertRTMinute = as.logical(args_vec[5]), # TRUE - FALSE
-  numDigitsMZ     = as.numeric(args_vec[6]), # Number of digits MZ
-  numDigitsRT     = as.numeric(args_vec[7]) # Number of digits RT
+  numDigitsMZ = as.numeric(args_vec[6]), # Number of digits MZ
+  numDigitsRT = as.numeric(args_vec[7]), # Number of digits RT
+  singlefile_galaxyPath = args_vec[8], # @COMMAND_FILE_LOAD@
+  singlefile_sampleName = args_vec[9] # @COMMAND_FILE_LOAD@
 )
 
 print("Converted arguments:")