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Changeset 1:cbea5e9fd0b4 (2017-05-23)

Previous changeset 0:68e2d63bece0 (2017-05-05) Next changeset 2:5e64657b4fe5 (2018-03-28)

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Uploaded

modified:
nmr_preprocessing/NmrPreprocessing_script.R
nmr_preprocessing/NmrPreprocessing_wrapper.R
nmr_preprocessing/NmrPreprocessing_xml.xml

diff -r 68e2d63bece0 -r cbea5e9fd0b4 nmr_preprocessing/NmrPreprocessing_script.R
--- a/nmr_preprocessing/NmrPreprocessing_script.R Fri May 05 07:13:02 2017 -0400
+++ b/nmr_preprocessing/NmrPreprocessing_script.R Tue May 23 03:32:51 2017 -0400

[

b'@@ -550,7 +550,7 @@\n # InternalReferencing \n ## ====================================================\n \n-InternalReferencing <- function(RawSpect_data, RawSpect_info, method = c("max", "thres"), \n+InternalReferencing <- function(Spectrum_data, Fid_info, method = c("max", "thres"), \n range = c("near0", "all", "window"), ppm.ref = 0, \n shiftHandling = c("zerofilling", "cut", "NAfilling", \n "circular"), c = 2, pc = 0.02, fromto.RC = NULL,\n@@ -560,9 +560,9 @@\n \n # Data initialisation and checks ----------------------------------------------\n \n- begin_info <- beginTreatment("InternalReferencing", RawSpect_data, RawSpect_info)\n- RawSpect_data <- begin_info[["Signal_data"]]\n- RawSpect_info <- begin_info[["Signal_info"]]\n+ begin_info <- beginTreatment("InternalReferencing", Spectrum_data, Fid_info)\n+ Spectrum_data <- begin_info[["Signal_data"]]\n+ Fid_info <- begin_info[["Signal_info"]]\n \n \n # Check input arguments\n@@ -582,9 +582,9 @@\n if (!is.null(fromto.RC)) {\n diff <- diff(unlist(fromto.RC))[1:length(diff(unlist(fromto.RC)))%%2 !=0]\n for (i in 1:length(diff)) {\n- if (diff[i] <= 0) {\n- stop(paste("Invalid region removal because from > to"))\n- }\n+ if (ppm == TRUE & diff[i] >= 0) {\n+ stop(paste("Invalid region removal because from <= to in ppm"))\n+ } else if (ppm == FALSE & diff[i] <= 0) {stop(paste("Invalid region removal because from >= to in column index"))}\n }\n }\n \n@@ -627,15 +627,15 @@\n # Apply the method (\'thres\' or \'max\') on spectra\n # ----------------------------------------------\n \n- n <- nrow(RawSpect_data)\n- m <- ncol(RawSpect_data)\n+ n <- nrow(Spectrum_data)\n+ m <- ncol(Spectrum_data)\n \n # The Sweep Width has to be the same since the column names are the same\n- SW <- RawSpect_info[1, "SW"] # Sweep Width in ppm (semi frequency scale in ppm)\n+ SW <- Fid_info[1, "SW"] # Sweep Width in ppm (semi frequency scale in ppm)\n ppmInterval <- SW/m # FIXME divide by two ??\n \n if (range == "all") {\n- Data <- RawSpect_data\n+ Data <- Spectrum_data\n } else {\n if (range == "near0") {\n fromto.RC <- list(c(-(SW * pc)/2, (SW * pc)/2)) # automatic fromto values in ppm\n@@ -644,7 +644,7 @@\n # if ppm == TRUE, then fromto is in the colnames values, else, in the column\n # index\n if (ppm == TRUE) {\n- colindex <- as.numeric(colnames(RawSpect_data))\n+ colindex <- as.numeric(colnames(Spectrum_data))\n } else {\n colindex <- 1:m\n }\n@@ -659,9 +659,9 @@\n vector <- rep(0, m)\n vector[unlist(Int)] <- 1\n if (n > 1) {\n- Data <- sweep(RawSpect_data, MARGIN = 2, FUN = "*", vector) # Cropped_Spectrum\n+ Data <- sweep(Spectrum_data, MARGIN = 2, FUN = "*", vector) # Cropped_Spectrum\n } else {\n- Data <- RawSpect_data * vector\n+ Data <- Spectrum_data * vector\n } # Cropped_Spectrum\n }\n \n@@ -701,17 +701,17 @@\n \n ppmScale <- ppmScale + ppm.ref\n \n- Spectrum_data <- matrix(fill, nrow = n, ncol = -(end - start) + 1, \n- dimnames = list(rownames(RawSpect_data), ppmScale))\n+ Spectrum_data_calib <- matrix(fill, nrow = n, ncol = -(end - start) + 1, \n+ dimnames = list(rownames(Spectrum_data), ppmScale))\n for (i in 1:n) {\n shift <- (1 - TMSPpeaks[i]) + start\n- Spectrum_data[i, (1 + shift):(m + shift)] <- RawSpect_data[i, ]\n+ Spectrum_data_calib[i, (1 + shift):(m + shift)] <- Spectrum_data[i, ]\n }\n \n if (shiftHandling == "cut") {\n- Spectrum_data = as.matrix(stats::na.omit(t(Spectrum_data)))\n- Spectrum_data = t(Spectrum_data)\n- base::attr(Spectrum_data, "na.action") <- NULL\n+ Spectrum_data_calib = as.matrix(stats::na.omit(t(Spectrum_data_calib)))\n+ Spectrum_data_calib = t(Spectrum_data_calib)\n+ base::attr(Spectrum_data_calib,'..b'"Invalid region removal because from <= to in ppm"))\n+ } else if (ppm == FALSE & diff[i] <= 0) {stop(paste("Invalid region removal because from >= to in column index"))}\n }\n \n- Int <- vector("list", length(fromto.0OPC))\n- for (i in 1:length(fromto.0OPC)) {\n- Int[[i]] <- indexInterval(colindex, from = fromto.0OPC[[i]][1], \n- to = fromto.0OPC[[i]][2], inclusive = TRUE)\n+ \n+ Int <- vector("list", length(exclude))\n+ for (i in 1:length(exclude)) {\n+ Int[[i]] <- indexInterval(colindex, from = exclude[[i]][1], \n+ to = exclude[[i]][2], inclusive = TRUE)\n }\n \n- vector <- rep(0, m)\n- vector[unlist(Int)] <- 1\n+ vector <- rep(1, m)\n+ vector[unlist(Int)] <- 0\n if (n > 1) {\n Data <- sweep(Spectrum_data, MARGIN = 2, FUN = "*", vector) # Cropped_Spectrum\n } else {\n@@ -953,8 +940,8 @@\n # work in either [-pi;pi] or [0;2pi] (this is not easy to be convinced by that I\n # agree) and we can check which one it is simply by the following trick\n \n- f0 <- rms(0, Data[k, ], p = quant, meth = method)\n- fpi <- rms(pi, Data[k, ], p = quant, meth = method)\n+ f0 <- rms(0, Data[k, ],meth = method)\n+ fpi <- rms(pi, Data[k, ], meth = method)\n if (f0 < fpi) {\n interval <- c(-pi, pi)\n } else {\n@@ -967,7 +954,7 @@\n x <- seq(min(interval), max(interval), length.out = 100)\n y <- rep(1, 100)\n for (K in (1:100)) {\n- y[K] <- rms(x[K], Data[k, ], p = quant, meth = method)\n+ y[K] <- rms(x[K], Data[k, ], meth = method)\n }\n if (createWindow == TRUE) {\n grDevices::dev.new(noRStudioGD = FALSE)\n@@ -978,7 +965,7 @@\n \n # Best angle\n best <- stats::optimize(rms, interval = interval, maximum = TRUE, \n- y = Data[k,], p = quant, meth = method)\n+ y = Data[k,], meth = method)\n ang <- best[["maximum"]]\n \n \n@@ -1011,32 +998,12 @@\n stop(paste("angle has length", length(angle), "and there are", n, "spectra to rotate."))\n }\n for (k in 1:n) {\n- Spectrum_data[k, ] <- Spectrum_data[k, ] * exp(complex(real = 0, imaginary = ang))\n+ Spectrum_data[k, ] <- Spectrum_data[k, ] * exp(complex(real = 0, imaginary = - angle[k]))\n }\n }\n \n \n \n- # #================== Detect a 180\xc2\xb0 rotation due to the water signal MEAN_Q = c()\n- # for (i in 1:nrow(Spectrum_data)) { data = Re(Spectrum_data[i,]) data_p =\n- # data[data >= stats::quantile(data[data >=0 ], p.zo)] data_n = data[data <=\n- # stats::quantile(data[data <0 ], (1-p.zo))] mean_quant = (sum(data_p) +\n- # sum(data_n)) / (length(data_p) +length(data_n)) # mean(p.zo% higher pos and neg\n- # values) MEAN_Q = c(MEAN_Q, mean_quant) } vect = which(MEAN_Q < 0) if\n- # (length(vect)!=0) { warning(\'The mean of\', p.zo,\' positive and negative\n- # quantiles is negative for \', paste0(rownames(Spectrum_data)[vect],\'; \'))\n- # if(rotation == TRUE) { warning(\' An automatic 180 degree rotation is applied to\n- # these spectra\') Angle[vect] = Angle[vect] + pi } } vect_risk =\n- # which(MEAN_Q<0.1*mean(MEAN_Q[MEAN_Q>0])) # is there any MEAN_Q with a very low\n- # value copared to mean of positive mean values? if (length(vect_risk)!=0)\n- # { warning(\'the rotation angle for spectra\',\n- # paste0(rownames(Spectrum_data)[vect_risk],\'; \'), \'might not be optimal, you\n- # need to check visually for those spectra\') } # result of automatic rotation for\n- # (k in vect_risk) { Spectrum_data[k,] <- Spectrum_data[k,] * exp(complex(real=0,\n- # imaginary=Angle[k])) } #==================\n- \n- \n- \n # Draw spectra\n if (plot_spectra == TRUE) {\n nn <- ceiling(n/4)\n@@ -1070,6 +1037,7 @@\n }\n \n \n+\n ## ====================================================\n # Baseline Correction \n ## ====================================================\n'

diff -r 68e2d63bece0 -r cbea5e9fd0b4 nmr_preprocessing/NmrPreprocessing_wrapper.R
--- a/nmr_preprocessing/NmrPreprocessing_wrapper.R Fri May 05 07:13:02 2017 -0400
+++ b/nmr_preprocessing/NmrPreprocessing_wrapper.R Tue May 23 03:32:51 2017 -0400

[

b'@@ -70,11 +70,22 @@\n ##======================================================\n ##======================================================\n \n+# graphical inputs\n+FirstOPCGraph <- argLs[["FirstOPCGraph"]]\n+SSGraph <- argLs[["SSGraph"]]\n+ApodGraph <- argLs[["ApodGraph"]]\n+FTGraph <- argLs[["FTGraph"]]\n+SRGraph <- argLs[["SRGraph"]]\n+ZeroOPCGraph <- argLs[["ZeroOPCGraph"]]\n+BCGraph <- argLs[["BCGraph"]]\n+FinalGraph <- argLs[["FinalGraph"]]\n+\n+\n # 1rst order phase correction ------------------------\n # Inputs\n \t## Data matrix\n Fid_data0 <- read.table(argLs[["dataMatrixFid"]],header=TRUE, check.names=FALSE, sep=\'\\t\')\n-Fid_data0 <- Fid_data0[,-1]\n+# Fid_data0 <- Fid_data0[,-1]\n Fid_data0 <- as.matrix(Fid_data0)\n \n \t## Samplemetadata\n@@ -120,7 +131,7 @@\n \n # Fourier transform ----------------------------------\n # Inputs\n-FTGraph <- argLs[["FTGraph"]]\n+\n \n # Internal referencering ----------------------------------\n # Inputs\n@@ -138,11 +149,11 @@\n # if (shiftReferencing=="YES")\n # {\n # \n-\tshiftReferencingMethod <- argLs[["shiftReferencingMethod"]]\n-\n-\tif (shiftReferencingMethod == "thres")\t{\n-\t\tshiftTreshold <- argLs[["shiftTreshold"]]\n-\t}\n+\t# shiftReferencingMethod <- argLs[["shiftReferencingMethod"]]\n+\t# \n+\t# if (shiftReferencingMethod == "thres")\t{\n+\t# \tshiftTreshold <- argLs[["shiftTreshold"]]\n+\t# }\n \t\n \tshiftReferencingRange <- argLs[["shiftReferencingRange"]]\n \t\n@@ -151,15 +162,18 @@\n \t}\n \t\n \tif (shiftReferencingRange == "window"){\n-\t shiftReferencingRangeList <- NULL\n-\t\tshiftReferencingRangeLeft <- argLs[["shiftReferencingRangeLeft"]]\n-\t\tshiftReferencingRangeRight <- argLs[["shiftReferencingRangeRight"]]\n-\t\tshiftReferencingRangeList <- list(shiftReferencingRangeList,c(shiftReferencingRangeLeft,shiftReferencingRangeRight))\n+\t shiftReferencingRangeList <- list()\n+\t for(i in which(names(argLs)=="shiftReferencingRangeLeft")) \n+\t {\n+ \t\tshiftReferencingRangeLeft <- argLs[[i]]\n+ \t\tshiftReferencingRangeRight <- argLs[[i+1]]\n+ \t\tshiftReferencingRangeList <- c(shiftReferencingRangeList,list(c(shiftReferencingRangeLeft,shiftReferencingRangeRight)))\n+\t }\n \t}\n \t\n \tshiftHandling <- argLs[["shiftHandling"]]\n \t\n-\tppm_ref <- argLs[["ppm_ref"]]\n+\n \t\n # }\n \n@@ -171,27 +185,24 @@\n createWindow = TRUE\n angle = NULL\n plot_spectra = FALSE\n-quant = 0.95\n ppm = TRUE\n-fromto.0OPC = NULL\n+exclude = NULL\n zeroOrderPhaseMethod <- argLs[["zeroOrderPhaseMethod"]]\n-if (zeroOrderPhaseMethod==\'rms\')\n-{\n- quant <- argLs[["quant"]]\n-}\n-if (zeroOrderPhaseMethod==\'max\')\n-{\n+\t\t\t\t\t\t\t\t\t\t \n+if (zeroOrderPhaseMethod==\'manual\'){\n angle <- argLs[["angle"]]\n }\n \n-searchZoneZeroPhase <- argLs[["searchZoneZeroPhase.choice"]]\n-if (searchZoneZeroPhase == "YES") {\n- searchZoneZeroPhaseList <- NULL\n- searchZoneZeroPhaseLeft <- argLs[["shiftReferencingRangeLeft"]]\n- searchZoneZeroPhaseRight <- argLs[["shiftReferencingRangeRight"]]\n- searchZoneZeroPhaseList <- list(searchZoneZeroPhaseList,c(searchZoneZeroPhaseLeft,searchZoneZeroPhaseRight))\n+excludeZoneZeroPhase <- argLs[["excludeZoneZeroPhase.choice"]]\n+if (excludeZoneZeroPhase == \'YES\') {\n+ excludeZoneZeroPhaseList <- list()\n+ for(i in which(names(argLs)=="excludeZoneZeroPhase_left")) {\n+ excludeZoneZeroPhaseLeft <- argLs[[i]]\n+ excludeZoneZeroPhaseRight <- argLs[[i+1]]\n+ excludeZoneZeroPhaseList <- c(excludeZoneZeroPhaseList,list(c(excludeZoneZeroPhaseLeft,excludeZoneZeroPhaseRight)))\n }\n-\n+ exclude <- excludeZoneZeroPhaseList\n+}\n \n \n # Baseline Correction -------------------------------\n@@ -235,20 +246,45 @@\n # FirstOrderPhaseCorrection ---------------------------------\n Fid_data <- FirstOrderPhaseCorrection(Fid_data0, Fid_info = samplemetadataFid, group_delay = NULL)\n \n+if (FirstOPCGraph == "YES") {\n+ title = "FIDs after First Order Phase Correction"\n+ DrawSignal(Fid_data, subtype = "stacked",\n+ ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n+ xlab = "Frequency", num.stacked = 4, \n+ main = title, createWindow=FALSE)\n+}\n \n # SolventSuppressi'..b'LSE, FALSE, FALSE), vertical = T, \n+ xlab = "Frequency", num.stacked = 4, \n+ main = title, createWindow=FALSE)\n+}\n+\n+\n # FourierTransform ---------------------------------\n Spectrum_data <- FourierTransform(Fid_data, Fid_info = samplemetadataFid, reverse.axis = TRUE)\n \n \n if (FTGraph == "YES") {\n- title = "Fourier transformed specta"\n+ title = "Fourier transformed spectra"\n DrawSignal(Spectrum_data, subtype = "stacked",\n ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n xlab = "Frequency", num.stacked = 4, \n@@ -257,45 +293,59 @@\n \n # InternalReferencing ---------------------------------\n # if (shiftReferencing=="YES") {\n-Spectrum_data <- InternalReferencing(Spectrum_data, samplemetadataFid, method = shiftReferencingMethod, range = shiftReferencingRange, \n+Spectrum_data <- InternalReferencing(Spectrum_data, samplemetadataFid, method = "max", range = shiftReferencingRange,\n ppm.ref = 0, shiftHandling = shiftHandling,ppm = TRUE,\n-\t\t\t\t\t\t\t\t\t\t\t c = shiftTreshold, fromto.RC = shiftReferencingRangeList, pc = pctNear0)\n+\t\t\t\t\t\t\t\t\t c = shiftTreshold, fromto.RC = shiftReferencingRangeList, pc = pctNear0)\n+\n+if (SRGraph == "YES") {\n+ title = "Spectra after Shift Referencing"\n+ DrawSignal(Spectrum_data, subtype = "stacked",\n+ ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n+ xlab = "Frequency", num.stacked = 4, \n+ main = title, createWindow=FALSE)\n+}\n \n # }\n \n # ZeroOrderPhaseCorrection ---------------------------------\n-Spectrum_data <- ZeroOrderPhaseCorrection(Spectrum_data, method = zeroOrderPhaseMethod, \n- plot_rms = plot_rms, returnAngle = returnAngle, \n- createWindow = createWindow,angle = angle, \n- plot_spectra = plot_spectra, quant = quant, \n- ppm = ppm, fromto.0OPC = fromto.0OPC)\n+Spectrum_data <- ZeroOrderPhaseCorrection(Spectrum_data, method = zeroOrderPhaseMethod,\n+ plot_rms = plot_rms, returnAngle = returnAngle,\n+ createWindow = createWindow,angle = angle,\n+ plot_spectra = plot_spectra,\n+ ppm = ppm, exclude = exclude)\n \n+if (ZeroOPCGraph == "YES") {\n title = "Spectra after Zero Order Phase Correction"\n DrawSignal(Spectrum_data, subtype = "stacked",\n ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n xlab = "Frequency", num.stacked = 4, \n main = title, createWindow=FALSE)\n+}\n \n # BaselineCorrection ---------------------------------\t\t\t\t\t\t\t\t\t \n-Spectrum_data <- BaselineCorrection(Spectrum_data, ptw.bc = TRUE, maxIter = maxIter, lambda.bc = lambdaBc, p.bc = pBc, eps = epsilon, returnBaseline = F) \n+Spectrum_data <- BaselineCorrection(Spectrum_data, ptw.bc = ptwBc, maxIter = maxIter, lambda.bc = lambdaBc, p.bc = pBc, eps = epsilon, returnBaseline = F) \n \n+if (BCGraph == "YES") {\n title = "Spectra after Baseline Correction"\n DrawSignal(Spectrum_data, subtype = "stacked",\n ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n xlab = "Frequency", num.stacked = 4, \n main = title, createWindow=FALSE)\n+}\n+\n \n # NegativeValuesZeroing ---------------------------------\n if (NegativetoZero=="YES") {\n+ Spectrum_data <- NegativeValuesZeroing(Spectrum_data)\n+}\n \n- Spectrum_data <- NegativeValuesZeroing(Spectrum_data)\n-\n- title = "Spectra after Negative Values Zeroing"\n+if (FinalGraph == "YES") {\n+ title = "Final preprocessed spectra"\n DrawSignal(Spectrum_data, subtype = "stacked",\n ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, \n xlab = "Frequency", num.stacked = 4, \n main = title, createWindow=FALSE)\n- }\n+}\n \n invisible(dev.off())\n \n'

diff -r 68e2d63bece0 -r cbea5e9fd0b4 nmr_preprocessing/NmrPreprocessing_xml.xml
--- a/nmr_preprocessing/NmrPreprocessing_xml.xml Fri May 05 07:13:02 2017 -0400
+++ b/nmr_preprocessing/NmrPreprocessing_xml.xml Tue May 23 03:32:51 2017 -0400

b'@@ -1,4 +1,4 @@\n-<tool id="NMR_Preprocessing" name="NMR_Preprocessing" version="3.0.1">\r\n+<tool id="NMR_Preprocessing" name="NMR_Preprocessing" version="3.1.0">\r\n \t<description> Preprocessing of 1D NMR spectra </description>\r\n \r\n <stdio>\r\n@@ -10,6 +10,8 @@\n Rscript $__tool_directory__/NmrPreprocessing_wrapper.R\r\n \r\n \t\t## First order phase correction\r\n+\t\t\t## Graphical display\r\n+\t\tFirstOPCGraph $FirstOPCGraph\r\n \t\t\t## Data matrix of FID spectra\r\n \t\tdataMatrixFid $dataMatrixFid\r\n \t\t\t## Sample metadata matrix\r\n@@ -20,9 +22,14 @@\n \t\t ## Smoothing parameter\r\n lambda $lambda\r\n \t\tptwSS $ptwSS\r\n+\t\t\t## Graphical display\r\n+\t\tSSGraph $SSGraph\r\n \t\t\r\n \t\t\r\n \t\t## Apodization\r\n+\t\t\t\t## Graphical display\r\n+\t\tApodGraph $ApodGraph\r\n+\t\r\n \t apodizationMethod $apodizationMethod.method\r\n \t\t #if $apodizationMethod.method == "exp":\r\n \t\t\t ## Line broadening for the exponential window\r\n@@ -54,18 +61,15 @@\n \t\t\t gaussLB $apodizationMethod.gaussLB \r\n \t\t #end if\r\n \t\r\n-\t\r\n \t\t## Fourier transform\r\n \t\t\t## Graphical display\r\n \t\t\tFTGraph $FTGraph\r\n \t\t\r\n \t\t\r\n \t\t## Shift referencing\r\n-\t\t\t## Method used to find the TMSP peaks in spectra\r\n-\t\t\tshiftReferencingMethod $shiftReferencingMethod.method\r\n-\t\t\t#if $shiftReferencingMethod.method == "thres":\r\n-\t\t\t\tshiftTreshold $shiftReferencingMethod.shiftTreshold\r\n-\t\t\t#end if\r\n+\t\t\t## Graphical display\r\n+\t\t\tSRGraph $SRGraph\r\n+\t\t\r\n \t\t\t## Definition of the search zone\r\n \t\t\tshiftReferencingRange $shiftReferencingRange.method\r\n \t\t\t#if $shiftReferencingRange.method == "near0":\r\n@@ -78,24 +82,27 @@\n \t #end for\r\n \t\t\t#end if\r\n \t\t\tshiftHandling $shiftHandling\r\n+\t\t\t\r\n \t\t\r\n \t\t\r\n \t\t## Zero order phase correction\r\n-\t\tzeroOrderPhaseMethod $zeroOrderPhaseMethod.method\r\n-\t #if $zeroOrderPhaseMethod.method == "rms":\r\n-\t\t\t ## Line broadening for the exponential window\r\n-\t\t\t quant $zeroOrderPhaseMethod.quant \r\n-\t\t#end if\r\n-\t\tsearchZoneZeroPhase.choice ${searchZoneZeroPhase.choice}\r\n- #if str($searchZoneZeroPhase.choice) == "YES":\r\n- #for $i in $searchZoneZeroPhase.conditions:\r\n- searchZoneZeroPhase_left ${i.searchZoneZeroPhase_left}\r\n- searchZoneZeroPhase_right ${i.searchZoneZeroPhase_right}\r\n+\t\t## Graphical display\r\n+\t\t\tZeroOPCGraph $ZeroOPCGraph\r\n+\t\t\t\r\n+\t\tzeroOrderPhaseMethod $zeroOrderPhaseMethod\r\n+\t\t\r\n+\t\texcludeZoneZeroPhase.choice ${excludeZoneZeroPhase.choice}\r\n+ #if str($excludeZoneZeroPhase.choice) == "YES":\r\n+ #for $i in $excludeZoneZeroPhase.conditions:\r\n+ excludeZoneZeroPhase_left ${i.excludeZoneZeroPhase_left}\r\n+ excludeZoneZeroPhase_right ${i.excludeZoneZeroPhase_right}\r\n #end for\r\n #end if\t\t\r\n \r\n \r\n \t\t## Baseline correction\r\n+\t\t## Graphical display\r\n+\t\t\tBCGraph $BCGraph\r\n \t\tptwBc $ptwBc\r\n \t\tmaxIter $maxIter\r\n \t\tlambdaBc $lambdaBc\r\n@@ -106,7 +113,11 @@\n \t\t## sets negative intensities to zero\r\n \t\tNegativetoZero $NegativetoZero\r\n \t\t\t\t\r\n-\t\t\r\n+\t\t## final spectra\r\n+\t\t## Graphical display\r\n+\t\t\tFinalGraph $FinalGraph\r\n+\t\t\t\r\n+\t\t\t\r\n ## Outputs\r\n dataMatrixOut $dataMatrixOut\r\n \t\tgraphOut $graphOut\r\n@@ -118,14 +129,28 @@\n \t\t<param name="dataMatrixFid" type="data" label="Data matrix of FIDs" help="" format="tabular" />\r\n \t\t<param name="sampleMetadataFid" type="data" label="Sample metadata matrix" help="" format="tabular" />\r\n \t\t\r\n- \t<param name="lambda" label="Smoothing parameter for solvent suppression" type="float" value="1000000" help="Default value is 1e6"/>\r\n+\t\t## First order phase correction\r\n+\t\t<param name="FirstOPCGraph" label="Display the FIDs after 1st order phase correction?" type="select" help="Select \'YES\' to display the spectra or \'NO\' to not display them ">\r\n+\t\t\t\t<option value="NO"> NO </option>\r\n+\t\t\t\t<option value="YES"> YES </option>\r\n+\t\t</param>\r\n+\t\t\t\t\r\n+\t\t## Water and / or solvents suppression\r\n+ \t<param name="lambda" label="Solvent Suppression: Smoothing parameter" type="float" value="1000000" help="Default value is 1e6"/>\r'..b'rrection: smoothing parameter" value="100000.0" help="Smoothing parameter, generally 1e5 \xe2\x80\x93 1e8. Default value is 100000" />\r\n+\t\t<param name="pBc" type="float" label="Baseline Correction: asymmetry parameter" value="0.05" help="Asymmetry parameter. Default value is 0.05" />\r\n+\t\t<param name="epsilon" type="float" label="Baseline Correction: numerical precision for convergence when estimating the baseline" value="0.00000001" help="Numerical precision for convergence when estimating the \tbaseline. Default value is 1e-8" />\r\n \t\t\r\n-\t\t<param name="maxIter" type="integer" label="Maximum of iterations if ptw.bc is set to FALSE" value="50" help="Maximum of iterations if ptw.bc is set to FALSE. Default value is 50" />\r\n-\t\t<param name="lambdaBc" type="float" label="Smoothing parameter" value="100000.0" help="Smoothing parameter, generally 1e5 \xe2\x80\x93 1e8. Default value is 100000" />\r\n-\t\t<param name="pBc" type="float" label="Asymmetry parameter" value="0.05" help="Asymmetry parameter. Default value is 0.05" />\r\n-\t\t<param name="epsilon" type="float" label="Numerical precision for convergence when estimating the baseline" value="0.00000001" help="Numerical precision for convergence when estimating the \tbaseline. Default value is 1e-8" />\r\n+\t\t<param name="BCGraph" label="Display the spectra after Baseline Correction?" type="select" help="Select \'YES\' to display the spectra or \'NO\' to not display them ">\r\n+\t\t\t\t<option value="NO"> NO </option>\r\n+\t\t\t\t<option value="YES"> YES </option>\r\n+\t\t</param>\r\n \t\t\r\n+\t\t\r\n+\t\t## NegativetoZero\r\n \t\t<param name="NegativetoZero" label="Set negative intensities to zero?" type="select" help="If YES, sets negative intensities to zero">\r\n \t\t\t<option value="NO"> NO </option>\r\n \t\t\t<option value="YES"> YES </option>\r\n \t\t</param>\r\n+\t\t\r\n+\t\t## final spectra\r\n+\t\t<param name="FinalGraph" label="Display the final spectra?" type="select" help="Select \'YES\' to display the spectra or \'NO\' to not display them ">\r\n+\t\t\t<option value="YES"> YES </option>\t\t\r\n+\t\t\t<option value="NO"> NO </option>\r\n+\t\t</param>\r\n+\t\t\r\n \t\t</inputs>\t\r\n \t\r\n \t<outputs>\r\n@@ -269,7 +313,7 @@\n \r\n These steps correspond to the following steps in the PEPS-NMR R library (https://github.com/ManonMartin/PEPSNMR):\r\n \r\n-* First order phase correction\r\n+* Group Delay suppression (First order phase correction)\r\n * Removal of solvent residuals signal from the FID\r\n * Apodization to increase the Signal-to-Noise ratio of the FID\r\n * Fourier transformation\r\n@@ -287,7 +331,6 @@\n \r\n The **types of apodization** are:\r\n \r\n-\r\n * exp: The signal is multiplied by a decreasing exponential exp(-t/LineBroadening).\r\n \r\n * cos2: The signal is multiplied by the value of a cosinus squared from 0 (where its value is 1) until pi/2 (where its value is 0).\r\n@@ -306,13 +349,6 @@\n **Shift referencing**\r\n ----------------------\r\n \r\n-Different **methods for shift referencing**:\r\n-\r\n-* max: the maximum intensity in the search zone is defined as the reference compound peak.\r\n-\r\n-* thres: the reference compound peak is the first peak in the spectrum higher than a predefined threshold (c) which is computed as: c*(cumulated_mean/cumulated_sd).\r\n-\r\n-\r\n The **searching window** can be adapted:\r\n \r\n * near0: the search concentrates around the 0ppm.\r\n@@ -333,8 +369,6 @@\n * cut: The ppm values for which some spectra are not defined are removed.\r\n \r\n \r\n-**ppm value of the reference compound**: By default, the ppm value of the reference compound is set to 0, but any arbitrary value in the ppm interval can be used instead.\r\n-\r\n \r\n **Zero Order Phase correction**\r\n -----------------------------------\r\n@@ -348,7 +382,7 @@\n * max: Optimization of the maximal spectral intensity.\r\n \r\n \r\n-**Search zone for the Zero order phase correction**: enables to optimize the criterion only on the selected spectral window(s).\r\n+** Exclusion area(s) for the Zero order phase correction**: enables to optimize the criterion with excluded spectral window(s), by default the water region is excluded.\r\n \r\n \r\n **Baseline computation**\r\n'