--- a/lib.r	Mon Jul 04 11:58:10 2016 -0400
+++ b/lib.r	Fri Apr 07 07:14:12 2017 -0400
@@ -1,323 +1,400 @@
-# lib.r ProbMetab version="1.0.0"
-# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
-# Contributors: Yann Guitton and Jean-francois Martin
-
-
-##Main probmetab function launch by the Galaxy ProbMetab wrapper
-probmetab = function(xa, xaP, xaN, variableMetadata, variableMetadataP, variableMetadataN, listArguments){
-	##ONE MODE ACQUISITION##
-	if(listArguments[["mode_acquisition"]]=="one") {
-		comb=NULL
-
-		#Get the polarity from xa object
-		polarity=xa@polarity
-		#SNR option
-		if ("xsetnofill" %in% names(listArguments)) {
-			load(listArguments[["xsetnofill"]])
-			xsetnofill=xset
-		}
-		else{
-			xsetnofill=NULL
-		}
-		#Exclude samples
-		if ("toexclude" %in% names(listArguments)) {
-			toexclude=listArguments[["toexclude"]]
-		}
-		else {
-			toexclude=NULL
-		}
-		ionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude)
-		comb=NULL
-	}
-
-	##TWO MODES ACQUISITION##
-	#Mode annotatediffreport
-	else if(listArguments[["inputs_mode"]]=="two"){
-		##Prepare the objects that will be used for the get.annot function
-		comb=1
-		
-
-		xsetPnofill=NULL
-		xsetNnofill=NULL
-		# TODO: a reactiver		
-		#if ("xsetPnofill" %in% names(listArguments)) {
-		#	load(listArguments[["xsetPnofill"]])
-		#	xsetPnofill=xset
-		#}
-		#if ("xsetNnofill" %in% names(listArguments)) {
-		#	load(listArguments[["xsetNnofill"]])
-		#	xsetNnofill=xset
-		#}
-		# include CAMERA non-annotated compounds, and snr retrieval 
-		# comb 2+ - used on Table 1	
-		ionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]]) 
-		ionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])
-		ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)
-		print(sum(ionAnnot$molIon[,3]==1))
-		print(sum(ionAnnot$molIon[,3]==0))
-		write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")
-		#Merge variableMetadata Negative and positive acquisitions mode
-		
-
-		#Mode combinexsannos TODO bug avec tableau issus de combinexsannos
-		#else {
-			#load(listArguments[["image_combinexsannos"]])
-			#image_combinexsannos=cAnnot
-			##Prepare the objects that will be used for the combineMolIon function
-			#load(listArguments[["image_pos"]])
-			#image_pos=xa
-			#ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos")
-		#}
-		
-	}
-
-	##DATABASE MATCHING##
-	if (listArguments[["kegg_db"]]=="KEGG"){		
-		DB=build.database.kegg(orgID = NULL)
-	}
-	else{	
-		table_list <<- NULL
-		ids=strsplit(listArguments[["kegg_db"]],",")
-		ids=ids[[1]]
-		if(length(ids)>1){
-			for(i in 1:length(ids)){
-				 table_list[[i]] <- build.database.kegg(ids[i])
-			}
-			db_table=do.call("rbind",table_list)
-			DB=unique(db_table)
-		}
-		else{
-			DB=build.database.kegg(listArguments[["kegg_db"]])
-		}
-	}	
-	#Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H)
-	reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
-	##PROBABILITY RANKING##
-	# number of masses with candidates inside the fixed mass window
-	# and masses with more than one candidate
-	length(unique(reactionM[reactionM[,"id"]!="unknown",1])) 
-	sum(table(reactionM[reactionM[,"id"]!="unknown",1])>1)
-	#if (listArguments[["useIso"]]){
-		#BUG TODO
-		# Calculate the ratio between observed and theoretical isotopic patterns.
-		# If you don't have an assessment of carbon offset to carbon number prediction 
-		# skip this step and use the reactionM as input to weigthM function. 
-		#isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB)  
-		#  calculate   the   likelihood   of   each   mass   to   compound   assignment   using   mass   accuracy,and isotopic pattern, when present
-		#wl < weightM(isoPatt,intervals=seq(0,1000,by=500), offset=c(3.115712, 3.434146, 2.350798))
-		
-			#isoPatt=incorporate.isotopes(ionAnnot, reactionM,comb=comb,var=listArguments[["var"]],DB=DB)
-
-		#wl = weightM(reactionM, useIso=true)
-	#}
-	#else {
-		#wl = weightM(reactionM, useIso=FALSE)
-	#}
-	wl =weightM(reactionM, useIso=FALSE)	
-	w = design.connection(reactionM)
-	# Probability calculations
-	x = 1:ncol(wl$wm)
-	y = 1:nrow(wl$wm)
-	conn = gibbs.samp(x, y, 5000, w, wl$wm)
-	ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
-	if(listArguments[["html"]]){
-		#Zip the EICS plot
-		system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"'))
-	}
-	
-	# calculate the correlations and partial correlations and cross reference then with reactions
-	mw=which(w==1,arr.ind=TRUE)
-	#reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial
-	#correlation in a user defined threshold of false discovery rate for significance testing. After the
-	#correlation test the function also overlay significant correlations with all putative reactions between
-	#two masses.
-	#It generates a list of estimated correlations and reactions.
-	corList=reac2cor(mw,ansConn$classTable,listArguments[["opt"]],listArguments[["corths"]],listArguments[["corprob"]],listArguments[["pcorprob"]])
-	ans=list("ansConn"=ansConn,"corList"=corList)
-	#Generate the siff table for CytoScape
-	cytoscape_output(corList,ansConn)
+# lib.r ProbMetab version="1.0.0"
+# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
+# Contributors: Yann Guitton and Jean-francois Martin
+
+
+##Main probmetab function launch by the Galaxy ProbMetab wrapper
+probmetab = function(xa, xaP, xaN, variableMetadata, variableMetadataP, variableMetadataN, listArguments){
+    ##ONE MODE ACQUISITION##
+    if(listArguments[["mode_acquisition"]]=="one") {
+        comb=NULL
+
+        #Get the polarity from xa object
+        polarity=xa@polarity
+        #SNR option
+        if ("xsetnofill" %in% names(listArguments)) {
+            load(listArguments[["xsetnofill"]])
+            xsetnofill=xset
+        }
+        else{
+            xsetnofill=NULL
+        }
+        #Exclude samples
+        if ("toexclude" %in% names(listArguments)) {
+            toexclude=listArguments[["toexclude"]]
+        }
+        else {
+            toexclude=NULL
+        }
+        ionAnnot=get.annot(xa, polarity=polarity, allowMiss=listArguments[["allowMiss"]],xset=xsetnofill,toexclude=toexclude)
+        comb=NULL
+    }
+
+    ##TWO MODES ACQUISITION##
+    #Mode annotatediffreport
+    else if(listArguments[["inputs_mode"]]=="two"){
+        ##Prepare the objects that will be used for the get.annot function
+        comb=1
+
+
+        xsetPnofill=NULL
+        xsetNnofill=NULL
+        # TODO: a reactiver
+        #if ("xsetPnofill" %in% names(listArguments)) {
+        #    load(listArguments[["xsetPnofill"]])
+        #    xsetPnofill=xset
+        #}
+        #if ("xsetNnofill" %in% names(listArguments)) {
+        #    load(listArguments[["xsetNnofill"]])
+        #    xsetNnofill=xset
+        #}
+        # include CAMERA non-annotated compounds, and snr retrieval
+        # comb 2+ - used on Table 1
+        ionAnnotP2plus = get.annot(xaP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]])
+        ionAnnotN2plus = get.annot(xaN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])
+        ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)
+        print(sum(ionAnnot$molIon[,3]==1))
+        print(sum(ionAnnot$molIon[,3]==0))
+        write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")
+        #Merge variableMetadata Negative and positive acquisitions mode
+
+
+        #Mode combinexsannos TODO bug avec tableau issus de combinexsannos
+        #else {
+            #load(listArguments[["image_combinexsannos"]])
+            #image_combinexsannos=cAnnot
+            ##Prepare the objects that will be used for the combineMolIon function
+            #load(listArguments[["image_pos"]])
+            #image_pos=xa
+            #ionAnnot=combineMolIon(peaklist=cAnnot, cameraobj=image_pos, polarity="pos")
+        #}
+
+    }
+
+    ##DATABASE MATCHING##
+    if (listArguments[["kegg_db"]]=="KEGG"){
+        DB=build.database.kegg(orgID = NULL)
+    }
+    else{
+        table_list <<- NULL
+        ids=strsplit(listArguments[["kegg_db"]],",")
+        ids=ids[[1]]
+        if(length(ids)>1){
+            for(i in 1:length(ids)){
+                 table_list[[i]] <- build.database.kegg(ids[i])
+            }
+            db_table=do.call("rbind",table_list)
+            DB=unique(db_table)
+        }
+        else{
+            DB=build.database.kegg(listArguments[["kegg_db"]])
+        }
+    }
+    #Matching des mass exactes mesurees avec les masses des compounds KEGG (pas M+H ou M-H)
+    reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
+    ##PROBABILITY RANKING##
+    # number of masses with candidates inside the fixed mass window
+    # and masses with more than one candidate
+    length(unique(reactionM[reactionM[,"id"]!="unknown",1]))
+    sum(table(reactionM[reactionM[,"id"]!="unknown",1])>1)
+    #if (listArguments[["useIso"]]){
+        #BUG TODO
+        # Calculate the ratio between observed and theoretical isotopic patterns.
+        # If you don't have an assessment of carbon offset to carbon number prediction
+        # skip this step and use the reactionM as input to weigthM function.
+        #isoPatt < incorporate.isotopes(comb2plus, reactionM, , samp=12:23, DB=DB)
+        #  calculate   the   likelihood   of   each   mass   to   compound   assignment   using   mass   accuracy,and isotopic pattern, when present
+        #wl < weightM(isoPatt,intervals=seq(0,1000,by=500), offset=c(3.115712, 3.434146, 2.350798))
+
+            #isoPatt=incorporate.isotopes(ionAnnot, reactionM,comb=comb,var=listArguments[["var"]],DB=DB)
+
+        #wl = weightM(reactionM, useIso=true)
+    #}
+    #else {
+        #wl = weightM(reactionM, useIso=FALSE)
+    #}
+    wl =weightM(reactionM, useIso=FALSE)
+    w = design.connection(reactionM)
+    # Probability calculations
+    x = 1:ncol(wl$wm)
+    y = 1:nrow(wl$wm)
+    conn = gibbs.samp(x, y, 5000, w, wl$wm)
+    ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
+    if(listArguments[["html"]]){
+        #Zip the EICS plot
+        system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"'))
+    }
+
+    # calculate the correlations and partial correlations and cross reference then with reactions
+    mw=which(w==1,arr.ind=TRUE)
+    #reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial
+    #correlation in a user defined threshold of false discovery rate for significance testing. After the
+    #correlation test the function also overlay significant correlations with all putative reactions between
+    #two masses.
+    #It generates a list of estimated correlations and reactions.
+    corList=reac2cor(mw,ansConn$classTable,listArguments[["opt"]],listArguments[["corths"]],listArguments[["corprob"]],listArguments[["pcorprob"]])
+    ans=list("ansConn"=ansConn,"corList"=corList)
+    #Generate the siff table for CytoScape
+    cytoscape_output(corList,ansConn)
 
 
-	#Execute the merge_probmetab function to merge the variableMetadata table and annotations from ProbMetab results
-	
-	if(listArguments[["mode_acquisition"]]=="one") {
-		#Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
-		names(variableMetadata)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt"
-		variableM=merge_probmetab(variableMetadata, ansConn)
-		write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
-	} else if (listArguments[["mode_acquisition"]]=="two") {
-		#Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
-		names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt"
-		names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz"
-		names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt"
-		variableMP=merge_probmetab(variableMetadataP, ansConn)
-		write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
-		variableMN=merge_probmetab(variableMetadataN, ansConn)
-		write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv")
-	}
-
-	return(ans)
-
-}
-
-##Function that generates a siff table for CytoScape
-cytoscape_output=function(corList,ansConn){
-	signif_cor=as.data.frame(corList$signif.cor)
-	classTable=as.data.frame(ansConn$classTable)
-	#Siff table
-	siff_table=cbind(signif_cor["node1"],signif_cor["cor"],signif_cor["node2"])
-	#attribute table output for Cytoscape
-
-	## START  Code part from the export2cytoscape function of ProbMetab written by Ricardo R. Silva 
-	for (i in 1:nrow(classTable)) if (classTable[i, 1] == ""){
-		classTable[i, c(1, 4, 6, 7)] <- classTable[i - 1, c(1, 4, 6, 7)]
-	}
- 	msel <- as.matrix(classTable[, 1:7])
- 	msel <- cbind(msel[, 6], msel[,-6])
- 	colnames(msel)[1] <- "Id"
- 	msel[, 1] <- sub("^\\s+", "", msel[, 1])
- 	colnames(msel)[1] <- "Id"
-	ids <- unique(msel[, 1])
- 	attrMatrix <- matrix("", nrow = length(ids), ncol = ncol(msel)-1)
-	for (i in 1:length(ids)) {
-		    attrMatrix[i, 1] <- unique(msel[msel[, 1] == ids[i], 
-		        2])
-		    attrMatrix[i, 2] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 3], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 3] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 4], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 4] <- unique(msel[msel[, 1] == ids[i], 
-		        5])
-		    attrMatrix[i, 5] <- paste("[", paste(msel[msel[, 
-		        1] == ids[i], 6], collapse = ", "), "]", sep = "")
-		    attrMatrix[i, 6] <- unique(msel[msel[, 1] == ids[i], 
-		        7])
-        }
-	ids <- as.numeric(unique(msel[, 1]))
-	attrMatrix <- cbind(ids, attrMatrix)
-	colnames(attrMatrix) <- colnames(msel)
-	## END Code part from the export2cytoscape function of ProbMetab writieen by Ricardo R. Silva 
-	write.table(attrMatrix, sep="\t", quote=FALSE, row.names=FALSE, file="Analysis_Report.tsv")
-	write.table(siff_table, sep="\t", quote=FALSE, row.names=FALSE, file="sif.tsv")
-
-	return(attrMatrix)
-}
-
-##Functions written by Jean-Francois Martin
-
-deter_ioni <- function (aninfo, pm)
-{
-  # determine ionisation in ProbMetab result file, used in function merge_probmetab
-  # input : for 1 ion, aninfo = string with m/z rt and CAMERA annotation from ProbMetab result file
-  # if the difference between m/z and the probmetab proposed mass is ~1 we use the sign (positive or negative) of this diference 
-  # to define the type of ionisation
-  # If adduct or fragment was detected, therefore diff >>1 and so, we search for substring "+" ou "2+" ou "3+" ou "-"... 
-  # to define the type of ionisation
-  # aninfo : vecteur of character resulting of the parsing(sep="#") of the probmetab annotation
-  if (round(abs(as.numeric(aninfo[1]) - pm),0) ==1) {
-    if (as.numeric(aninfo[1]) - pm <0) {esi <- "n"} else {esi <- "p"}
-  } else 
-    if (!is.na(aninfo[4])) {
-      anstr <- aninfo[4]
-      # cat(anstr)
-      if ((grepl("]+",anstr,fixed=T)==T) || (grepl("]2+",anstr,fixed=T)==T) || (grepl("]3+",anstr,fixed=T)==T)) { esi <- "p"}
-      else 
-        if ((grepl("]-",anstr,fixed=T)==T) || (grepl("]2-",anstr,fixed=T)==T) || (grepl("]3-",anstr,fixed=T)==T)) { esi <- "n"}
-      # cat(" ioni ",esi,"\n")
-    } else
-    { esi <- "u"} 
-  
-  return(esi)
-}
-
-
-merge_probmetab <- function(metaVar,ansConn) {
-  ## Parse ProbMetab information result file and merge in variable_metaData initial file
-  ##  inputs : 
-  ##      metaVar : data.frame of metadataVariable input of probmetab function
-  ##     ansConn  : data.frame of ProbMetab result
-  ## output : dataframe with Probmetab results merge with variableMetadata
-  ## Constante
-  ## iannot : indice de la colonne annotation dans le resultat de probMetab
-  iannot <- 4
-  
-  ## definition of an unique identification of ions mz with 3 decimals and rt(sec) with 1 decimal to avoid 
-  ## duplicate ions name in the diffreport result file
-  ions <- paste ("M",round(metaVar$mz,3),"T",round(metaVar$rt,1),sep="")
-  metaVar <- data.frame(ions,metaVar)
-  
-  ###### Result data.frame from ProbMetab result list
-  an_ini <- ansConn$classTable
-  
-  ## Suppression of rows without  mz and rt or unknown and columns of intensities
-  ## COLUMNS SUBSCRIPTS HAVE TO BE CHECKED WITh DIFFERENT RESULTS FILES 
-  an <- an_ini[(an_ini[,2]!="unknown"),c(1,2,3,7)]
-  ## initialisation of vectors receiving the result of the parse of the column annotation (subscrip iannot) 
-  mz <- rep(0,dim(an)[1])
-  rt <- rep(0,dim(an)[1])
-  propmz <- rep(0,dim(an)[1])
-  ioni <- rep("u",dim(an)[1])
-  
-  ## parse the column annotation and define ionisation mode
-  for (i in 1:dim(an)[1]) {
-    if (an[i,1] != "") {
-      info_mzrt <- unlist(strsplit(an[i,iannot],"#"))
-      propmz[i] <- as.numeric(an[i,1])
-      mz[i] <- as.numeric(info_mzrt[1])
-      rt[i] <- as.numeric(info_mzrt[2])
-      ioni[i] <- deter_ioni(info_mzrt,as.numeric(an[i,1]))
-    }
-    else {
-      propmz[i] <- as.numeric(propmz[i-1])
-      mz[i] <- as.numeric(mz[i-1])
-      rt[i] <- as.numeric(rt[i-1])
-      ioni[i] <- ioni[i-1]
-    }
-  }
-  
-  ## definition of an unique identification of ions : mz with 3 decimals and rt(sec) with 1 decimal
-  ## The same as for the metadataVariable data.frame to match with.
-  ions <- paste ("M",round(mz,3),"T",round(rt,1),sep="")
-  an <- data.frame(ions,ioni,propmz,mz,rt,an)
-  
-  ## transposition of the different probmetab annotations which are in different rows in the initial result data.frame
-  ## on only 1 row separated with a ";"
-  li <- as.matrix(table(an$propmz))
-  li <- data.frame(dimnames(li)[1],li)
-  dimnames(li)[[2]][1] <- "propmz"
-  ions   <- rep("u",dim(li)[1])
-  propmz <- rep(0,dim(li)[1])
-  mpc    <- rep("c",dim(li)[1])
-  proba  <- rep("p",dim(li)[1])
-  c <- 0
-  while (c < dim(li)[1]) {
-    c <- c + 1
-    suban     <- an[an$propmz==li[c,1],]
-    ions[c]   <- as.character(suban[1,1])
-    propmz[c] <- as.numeric(suban[1,3])
-    mpc[c]    <- paste(suban[,7],collapse=";")
-    proba[c]  <- paste(as.character(suban[,8]),collapse=";") 
-  }
-  
-  ## Creation of the data.frame with 1 row per ions
-  anc <- data.frame(ions,propmz,mpc,proba)
-  anc <- anc[order(anc[,1]),]
-  
-  metaVarFinal <- merge(metaVar, anc, by.x=1, by.y=1, all.x=T, all.y=T)
-  metaVarFinal <- metaVarFinal[,-1]
-  #write.table(metaVarFinal,file="res.txt", sep="\t", row.names=F, quote=F)
-  
-  return (metaVarFinal)
-}
+    #Execute the merge_probmetab function to merge the variableMetadata table and annotations from ProbMetab results
+
+    if(listArguments[["mode_acquisition"]]=="one") {
+        #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
+        names(variableMetadata)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt"
+        variableM=merge_probmetab(variableMetadata, ansConn)
+        write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
+    } else if (listArguments[["mode_acquisition"]]=="two") {
+        #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
+        names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt"
+        names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz"
+        names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt"
+        variableMP=merge_probmetab(variableMetadataP, ansConn)
+        write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
+        variableMN=merge_probmetab(variableMetadataN, ansConn)
+        write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv")
+    }
+
+    return(ans)
+
+}
+
+##Function that generates a siff table for CytoScape
+cytoscape_output=function(corList,ansConn){
+    signif_cor=as.data.frame(corList$signif.cor)
+    classTable=as.data.frame(ansConn$classTable)
+    #Siff table
+    siff_table=cbind(signif_cor["node1"],signif_cor["cor"],signif_cor["node2"])
+    #attribute table output for Cytoscape
+
+    ## START  Code part from the export2cytoscape function of ProbMetab written by Ricardo R. Silva
+    for (i in 1:nrow(classTable)) if (classTable[i, 1] == ""){
+        classTable[i, c(1, 4, 6, 7)] <- classTable[i - 1, c(1, 4, 6, 7)]
+    }
+     msel <- as.matrix(classTable[, 1:7])
+     msel <- cbind(msel[, 6], msel[,-6])
+     colnames(msel)[1] <- "Id"
+     msel[, 1] <- sub("^\\s+", "", msel[, 1])
+     colnames(msel)[1] <- "Id"
+    ids <- unique(msel[, 1])
+     attrMatrix <- matrix("", nrow = length(ids), ncol = ncol(msel)-1)
+    for (i in 1:length(ids)) {
+            attrMatrix[i, 1] <- unique(msel[msel[, 1] == ids[i],
+                2])
+            attrMatrix[i, 2] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 3], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 3] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 4], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 4] <- unique(msel[msel[, 1] == ids[i],
+                5])
+            attrMatrix[i, 5] <- paste("[", paste(msel[msel[,
+                1] == ids[i], 6], collapse = ", "), "]", sep = "")
+            attrMatrix[i, 6] <- unique(msel[msel[, 1] == ids[i],
+                7])
+        }
+    ids <- as.numeric(unique(msel[, 1]))
+    attrMatrix <- cbind(ids, attrMatrix)
+    colnames(attrMatrix) <- colnames(msel)
+    ## END Code part from the export2cytoscape function of ProbMetab writieen by Ricardo R. Silva
+    write.table(attrMatrix, sep="\t", quote=FALSE, row.names=FALSE, file="Analysis_Report.tsv")
+    write.table(siff_table, sep="\t", quote=FALSE, row.names=FALSE, file="sif.tsv")
+
+    return(attrMatrix)
+}
+
+##Functions written by Jean-Francois Martin
+
+deter_ioni <- function (aninfo, pm)
+{
+  # determine ionisation in ProbMetab result file, used in function merge_probmetab
+  # input : for 1 ion, aninfo = string with m/z rt and CAMERA annotation from ProbMetab result file
+  # if the difference between m/z and the probmetab proposed mass is ~1 we use the sign (positive or negative) of this diference
+  # to define the type of ionisation
+  # If adduct or fragment was detected, therefore diff >>1 and so, we search for substring "+" ou "2+" ou "3+" ou "-"...
+  # to define the type of ionisation
+  # aninfo : vecteur of character resulting of the parsing(sep="#") of the probmetab annotation
+  if (round(abs(as.numeric(aninfo[1]) - pm),0) ==1) {
+    if (as.numeric(aninfo[1]) - pm <0) {esi <- "n"} else {esi <- "p"}
+  } else
+    if (!is.na(aninfo[4])) {
+      anstr <- aninfo[4]
+      # cat(anstr)
+      if ((grepl("]+",anstr,fixed=T)==T) || (grepl("]2+",anstr,fixed=T)==T) || (grepl("]3+",anstr,fixed=T)==T)) { esi <- "p"}
+      else
+        if ((grepl("]-",anstr,fixed=T)==T) || (grepl("]2-",anstr,fixed=T)==T) || (grepl("]3-",anstr,fixed=T)==T)) { esi <- "n"}
+      # cat(" ioni ",esi,"\n")
+    } else
+    { esi <- "u"}
+
+  return(esi)
+}
+
+
+merge_probmetab <- function(metaVar,ansConn) {
+  ## Parse ProbMetab information result file and merge in variable_metaData initial file
+  ##  inputs :
+  ##      metaVar : data.frame of metadataVariable input of probmetab function
+  ##     ansConn  : data.frame of ProbMetab result
+  ## output : dataframe with Probmetab results merge with variableMetadata
+  ## Constante
+  ## iannot : indice de la colonne annotation dans le resultat de probMetab
+  iannot <- 4
+
+  ## definition of an unique identification of ions mz with 3 decimals and rt(sec) with 1 decimal to avoid
+  ## duplicate ions name in the diffreport result file
+  ions <- paste ("M",round(metaVar$mz,3),"T",round(metaVar$rt,1),sep="")
+  metaVar <- data.frame(ions,metaVar)
+
+  ###### Result data.frame from ProbMetab result list
+  an_ini <- ansConn$classTable
+
+  ## Suppression of rows without  mz and rt or unknown and columns of intensities
+  ## COLUMNS SUBSCRIPTS HAVE TO BE CHECKED WITh DIFFERENT RESULTS FILES
+  an <- an_ini[(an_ini[,2]!="unknown"),c(1,2,3,7)]
+  ## initialisation of vectors receiving the result of the parse of the column annotation (subscrip iannot)
+  mz <- rep(0,dim(an)[1])
+  rt <- rep(0,dim(an)[1])
+  propmz <- rep(0,dim(an)[1])
+  ioni <- rep("u",dim(an)[1])
+
+  ## parse the column annotation and define ionisation mode
+  for (i in 1:dim(an)[1]) {
+    if (an[i,1] != "") {
+      info_mzrt <- unlist(strsplit(an[i,iannot],"#"))
+      propmz[i] <- as.numeric(an[i,1])
+      mz[i] <- as.numeric(info_mzrt[1])
+      rt[i] <- as.numeric(info_mzrt[2])
+      ioni[i] <- deter_ioni(info_mzrt,as.numeric(an[i,1]))
+    }
+    else {
+      propmz[i] <- as.numeric(propmz[i-1])
+      mz[i] <- as.numeric(mz[i-1])
+      rt[i] <- as.numeric(rt[i-1])
+      ioni[i] <- ioni[i-1]
+    }
+  }
+
+  ## definition of an unique identification of ions : mz with 3 decimals and rt(sec) with 1 decimal
+  ## The same as for the metadataVariable data.frame to match with.
+  ions <- paste ("M",round(mz,3),"T",round(rt,1),sep="")
+  an <- data.frame(ions,ioni,propmz,mz,rt,an)
+
+  ## transposition of the different probmetab annotations which are in different rows in the initial result data.frame
+  ## on only 1 row separated with a ";"
+  li <- as.matrix(table(an$propmz))
+  li <- data.frame(dimnames(li)[1],li)
+  dimnames(li)[[2]][1] <- "propmz"
+  ions   <- rep("u",dim(li)[1])
+  propmz <- rep(0,dim(li)[1])
+  mpc    <- rep("c",dim(li)[1])
+  proba  <- rep("p",dim(li)[1])
+  c <- 0
+  while (c < dim(li)[1]) {
+    c <- c + 1
+    suban     <- an[an$propmz==li[c,1],]
+    ions[c]   <- as.character(suban[1,1])
+    propmz[c] <- as.numeric(suban[1,3])
+    mpc[c]    <- paste(suban[,7],collapse=";")
+    proba[c]  <- paste(as.character(suban[,8]),collapse=";")
+  }
+
+  ## Creation of the data.frame with 1 row per ions
+  anc <- data.frame(ions,propmz,mpc,proba)
+  anc <- anc[order(anc[,1]),]
+
+  metaVarFinal <- merge(metaVar, anc, by.x=1, by.y=1, all.x=T, all.y=T)
+  metaVarFinal <- metaVarFinal[,-1]
+  #write.table(metaVarFinal,file="res.txt", sep="\t", row.names=F, quote=F)
+
+  return (metaVarFinal)
+}
 
 # RETROCOMPATIBILITE avec ancienne version de annotate
 getVariableMetadata = function(xa) {
-	# --- variableMetadata ---
-	peakList=getPeaklist(xa)
-	peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
-	variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))]
-	variableMetadata$name= paste("M",round(variableMetadata$mz),"T",round(variableMetadata$rt),sep="")
-	return (variableMetadata)
-}
+    # --- variableMetadata ---
+    peakList=getPeaklist(xa)
+    peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
+    variableMetadata=peakList[,!(colnames(peakList) %in% c(sampnames(xa@xcmsSet)))]
+    variableMetadata$name= groupnames(xa@xcmsSet)
+    return (variableMetadata)
+}
+
+
+# This function get the raw file path from the arguments
+getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
+    if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
+    if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
+    if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]
+
+    if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
+    }
+    if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
+    }
+    if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
+        singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
+        singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
+    }
+    if (exists("singlefile_galaxyPaths")){
+        singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
+        singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
+
+        singlefile=NULL
+        for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
+            singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
+            singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
+            singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
+        }
+    }
+    return(list(zipfile=zipfile, singlefile=singlefile))
+}
+
+
+# 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
+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
+
+    if(!is.null(singlefile) && (length("singlefile")>0)) {
+        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)
+            }
+
+            file.symlink(singlefile_galaxyPath,singlefile_sampleName)
+        }
+        directory = "."
+
+    }
+    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)
+        }
+
+        #list all file in the zip file
+        #zip_files=unzip(zipfile,list=T)[,"Name"]
+
+        #unzip
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
+
+        #get the directory name
+        filesInZip=unzip(zipfile, list=T);
+        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")
+
+    }
+}