diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R
index 2ae5283b5..9272249d2 100755
--- a/tools/camera/CAMERA_findAdducts.R
+++ b/tools/camera/CAMERA_findAdducts.R
@@ -23,8 +23,8 @@ args <- list(
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
- singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
- singlefile_sampleName = args_vec[14] # @COMMAND_FILE_LOAD@
+ singlefile_galaxyPath = args_vec[14], # @COMMAND_FILE_LOAD@
+ singlefile_sampleName = args_vec[16] # @COMMAND_FILE_LOAD@
)
# Check if the 'rules' argument in 'args' is NULL
@@ -198,7 +198,7 @@ ncols <- length(colnames(peakList))
sample_cols <- length(xa@sample) # Number of samples
# Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
# Combine the selected columns from matgrp with the group names
diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R
index 9c1511700..18491b98a 100755
--- a/tools/camera/CAMERA_findIsotopes.R
+++ b/tools/camera/CAMERA_findIsotopes.R
@@ -22,8 +22,8 @@ args <- list(
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
- singlefile_galaxyPath = args_vec[12], # @COMMAND_FILE_LOAD@
- singlefile_sampleName = args_vec[13] # @COMMAND_FILE_LOAD@
+ singlefile_galaxyPath = args_vec[13], # @COMMAND_FILE_LOAD@
+ singlefile_sampleName = args_vec[15] # @COMMAND_FILE_LOAD@
)
print("Converted arguments:")
@@ -196,7 +196,7 @@ ncols <- length(colnames(peakList))
sample_cols <- length(xa@sample) # Number of samples
# Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
# Combine the selected columns from matgrp with the group names
diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R
index 7f98537b1..331ed887f 100755
--- a/tools/camera/CAMERA_groupCorr.R
+++ b/tools/camera/CAMERA_groupCorr.R
@@ -23,8 +23,8 @@ args <- list(
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@
+ singlefile_galaxyPath = args_vec[14], # @COMMAND_FILE_LOAD@
+ singlefile_sampleName = args_vec[16] # @COMMAND_FILE_LOAD@
)
print("Converted arguments:")
@@ -171,7 +171,7 @@ ncols <- length(colnames(peakList))
sample_cols <- length(xa@sample) # Number of samples
# Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
# Combine the selected columns from matgrp with the group names
diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R
index 5f7d659d6..ecfeed0fb 100755
--- a/tools/camera/CAMERA_groupFWHM.R
+++ b/tools/camera/CAMERA_groupFWHM.R
@@ -19,8 +19,8 @@ args <- list(
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
- singlefile_galaxyPath = args_vec[8], # @COMMAND_FILE_LOAD@
- singlefile_sampleName = args_vec[9] # @COMMAND_FILE_LOAD@
+ singlefile_galaxyPath = args_vec[9], # @COMMAND_FILE_LOAD@
+ singlefile_sampleName = args_vec[11] # @COMMAND_FILE_LOAD@
)
print("Converted arguments:")
@@ -186,7 +186,7 @@ ncols <- length(colnames(peakList))
sample_cols <- length(xa@sample) # Number of samples
# Indices for the columns of interest
-main_cols <- 1:(ncols - (3 + sample_cols)) # Main columns before sample columns
+main_cols <- 1:(ncols - (6 + sample_cols)) # Main columns before sample columns
tail_cols <- (ncols - 2):ncols # The last 3 columns (adduct, isotope, pcgroup)
# Combine the selected columns from matgrp with the group names
diff --git a/tools/camera/findAdducts.xml b/tools/camera/findAdducts.xml
index b59775282..5355a25f6 100755
--- a/tools/camera/findAdducts.xml
+++ b/tools/camera/findAdducts.xml
@@ -111,7 +111,7 @@
-
+
-
-
+
+
-
+
-
-
+
+
-
+
-
-
+
+
-
+
-
-
+
+