Mercurial > repos > yguitton > metams_rungc

changeset 3:c75532b75ba1 draft

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Uploaded version 2.1.1
author yguitton
date Thu, 08 Jun 2017 11:53:35 -0400
parents 8e1b99a7d733
children c10824185547
files lib_metams.r metams.r metams_runGC.xml
diffstat 3 files changed, 388 insertions(+), 251 deletions(-) [+]
line wrap: on
line diff
--- a/lib_metams.r	Wed May 24 07:39:18 2017 -0400
+++ b/lib_metams.r	Thu Jun 08 11:53:35 2017 -0400
@@ -1,6 +1,7 @@
-# lib_metams.r version 0.99.6
+# lib_metams.r version 2.0.0
 # R function for metaMS runGC under W4M
 # author Yann GUITTON CNRS IRISA/LINA Idealg project 2014-2015
+# author Yann GUITTON Oniris Laberca 2015-2017
 
 
 ##ADDITIONS FROM Y. Guitton
@@ -245,249 +246,335 @@
     ##Annotation table each value is a pcgrp associated to the unknown 
     ##NOTE pcgrp index are different between xcmsSet and resGC due to filtering steps in metaMS
     ##R. Wehrens give me some clues on that and we found a correction
- 
-    mat<-matrix(ncol=length(resGC$xset), nrow=dim(resGC$PeakTable)[1])
-     
-    for (j in 1: length(resGC$xset)){
-        test<-resGC$annotation[[j]]
-        print(paste("j=",j))
-        for (i in 1:dim(test)[1]){
-            if (as.numeric(row.names(test)[i])>dim(mat)[1]){
-                next
-            } else {
-                mat[as.numeric(row.names(test)[i]),j]<-test[i,1]
-            }
+    #if unkn="none"
+	
+	if(unkn=="none") {
+	   pdf("Unknown_Empty.pdf")
+	   plot.new()
+	   text(x=0.5,y=1,pos=1, labels="No EIC ploting required")
+	   dev.off()
+	}else {
+
+		mat<-matrix(ncol=length(resGC$xset), nrow=dim(resGC$PeakTable)[1])
+		 
+		for (j in 1: length(resGC$xset)){
+			test<-resGC$annotation[[j]]
+			print(paste("j=",j))
+			for (i in 1:dim(test)[1]){
+				if (as.numeric(row.names(test)[i])>dim(mat)[1]){
+					next
+				} else {
+					mat[as.numeric(row.names(test)[i]),j]<-test[i,1]
+				}
+			}
+		}
+		colnames(mat)<-colnames(resGC$PeakTable[,c((which(colnames(resGC$PeakTable)=="rt"|colnames(resGC$PeakTable)=="RI")[length(which(colnames(resGC$PeakTable)=="rt"|colnames(resGC$PeakTable)=="RI"))]+1):dim(resGC$PeakTable)[2])])
+		
+		#debug
+
+		# print(dim(mat))
+		# print(mat[1:3,]) 
+		# write.table(mat, file="myannotationtable.tsv", sep="\t", row.names=FALSE)
+		#correction of annotation matrix due to pcgrp removal by quality check in runGCresult
+		#matrix of correspondance between an@pspectra and filtered pspectra from runGC
+
+		allPCGRPs <-
+			lapply(1:length(resGC$xset),
+				function(i) {
+					an <- resGC$xset[[i]]
+					huhn <- an@pspectra[which(sapply(an@pspectra, length) >=
+					metaSetting(resGC$settings,
+					"DBconstruction.minfeat"))]
+					matCORR<-cbind(1:length(huhn), match(huhn, an@pspectra))
+				})
+
+		if (unkn[1]==""){    
+		#plot EIC and spectra for all unknown for comparative purpose
+	   
+
+			par (mar=c(5, 4, 4, 2) + 0.1)
+			for (l in 1:dim(resGC$PeakTable)[1]){ #l=2
+				#recordPlot
+				perpage=3 #if change change layout also!
+				num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
+				my.plots <- vector(num.plots, mode='list')
+				dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",l,".pdf", sep="")) #A4 pdf
+				# par(mfrow=c(perpage,2))
+				layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
+				# layout.show(6)
+				oma.saved <- par("oma")
+				par(oma = rep.int(0, 4))
+				par(oma = oma.saved)
+				o.par <- par(mar = rep.int(0, 4))
+				on.exit(par(o.par))
+				stop=0 #initialize
+				for (i in 1:num.plots) {
+					start=stop+1
+					stop=start+perpage-1 #
+					for (c in start:stop){
+						if (c <=dim(mat)[2]){
+								
+							#get sample name
+							sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
+
+							#remove .cdf, .mzXML filepattern
+							filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", 
+									"[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+							filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), 
+									collapse = "|")
+							sampname<-gsub(filepattern, "",sampname)
+							 
+							title1<-paste("unknown", l,"from",sampname, sep=" ")
+							an<-resGC$xset[[c]]
+							 
+							par (mar=c(0, 0, 0, 0) + 0.1)
+							plot.new()
+							box()
+							text(0.5, 0.5, title1, cex=2)
+							if (!is.na(mat[l,c])){
+								pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[l,c]),2]
+								if (pcgrp!=mat[l,c]) print ("pcgrp changed")
+								par (mar=c(3, 2.5, 3, 1.5) + 0.1)
+								plotEICs(an, pspec=pcgrp, maxlabel=2)
+								plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
+							} else {
+								plot.new()
+								box()
+								text(0.5, 0.5, "NOT FOUND", cex=2)
+								plot.new()
+								box()
+								text(0.5, 0.5, "NOT FOUND", cex=2)
+							}
+						}
+					 }
+					# my.plots[[i]] <- recordPlot()
+				}
+				graphics.off()
+
+					# pdf(file=paste("Unknown_",l,".pdf", sep=""), onefile=TRUE)
+					# for (my.plot in my.plots) {
+						# replayPlot(my.plot)
+					# }
+					# my.plots
+					# graphics.off()
+
+			}#end  for l
+		}#end if unkn=""
+		else{
+			par (mar=c(5, 4, 4, 2) + 0.1)
+			l=unkn
+			if (length(l)==1){
+				#recordPlot
+				perpage=3 #if change change layout also!
+				num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
+				my.plots <- vector(num.plots, mode='list')
+				
+				dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",l,".pdf", sep="")) #A4 pdf
+				# par(mfrow=c(perpage,2))
+				layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
+				# layout.show(6)
+				oma.saved <- par("oma")
+				par(oma = rep.int(0, 4))
+				par(oma = oma.saved)
+				o.par <- par(mar = rep.int(0, 4))
+				on.exit(par(o.par))
+				stop=0 #initialize
+				for (i in 1:num.plots) {
+					start=stop+1
+					stop=start+perpage-1 #
+					for (c in start:stop){
+						if (c <=dim(mat)[2]){
+								
+							#get sample name
+							sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
+
+							#remove .cdf, .mzXML filepattern
+							filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+							filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
+							sampname<-gsub(filepattern, "",sampname)
+							 
+							title1<-paste("unknown", l,"from",sampname, sep=" ")
+							an<-resGC$xset[[c]]
+							 
+							par (mar=c(0, 0, 0, 0) + 0.1)
+							plot.new()
+							box()
+							text(0.5, 0.5, title1, cex=2)
+							if (!is.na(mat[l,c])){
+								pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[l,c]),2]
+								if (pcgrp!=mat[l,c]) print ("pcgrp changed")
+								par (mar=c(3, 2.5, 3, 1.5) + 0.1)
+								plotEICs(an, pspec=pcgrp, maxlabel=2)
+								plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
+							} else {
+								plot.new()
+								box()
+								text(0.5, 0.5, "NOT FOUND", cex=2)
+								plot.new()
+								box()
+								text(0.5, 0.5, "NOT FOUND", cex=2)
+							}
+						}
+					}
+					# my.plots[[i]] <- recordPlot()
+				}
+				graphics.off()
+
+				# pdf(file=paste("Unknown_",l,".pdf", sep=""), onefile=TRUE)
+				# for (my.plot in my.plots) {
+					# replayPlot(my.plot)
+				# }
+				# my.plots
+				# graphics.off()
+			} else {
+				par (mar=c(5, 4, 4, 2) + 0.1)
+				for (l in 1:length(unkn)){ #l=2
+					#recordPlot
+					perpage=3 #if change change layout also!
+					num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
+					my.plots <- vector(num.plots, mode='list')
+					dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",unkn[l],".pdf", sep="")) #A4 pdf
+					# par(mfrow=c(perpage,2))
+					layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
+					# layout.show(6)
+					oma.saved <- par("oma")
+					par(oma = rep.int(0, 4))
+					par(oma = oma.saved)
+					o.par <- par(mar = rep.int(0, 4))
+					on.exit(par(o.par))
+					stop=0 #initialize
+					for (i in 1:num.plots) {
+						start=stop+1
+						stop=start+perpage-1 #
+						for (c in start:stop){
+							if (c <=dim(mat)[2]){
+							
+								#get sample name
+								sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
+
+								#remove .cdf, .mzXML filepattern
+								filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+								filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
+								sampname<-gsub(filepattern, "",sampname)
+								 
+								title1<-paste("unknown",unkn[l],"from",sampname, sep=" ")
+								an<-resGC$xset[[c]]
+								 
+								par (mar=c(0, 0, 0, 0) + 0.1)
+								plot.new()
+								box()
+								text(0.5, 0.5, title1, cex=2)
+								if (!is.na(mat[unkn[l],c])){
+									pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[unkn[l],c]),2]
+									if (pcgrp!=mat[unkn[l],c]) print ("pcgrp changed")
+									par (mar=c(3, 2.5, 3, 1.5) + 0.1)
+									plotEICs(an, pspec=pcgrp, maxlabel=2)
+									plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
+								} else {
+									plot.new()
+									box()
+									text(0.5, 0.5, "NOT FOUND", cex=2)
+									plot.new()
+									box()
+									text(0.5, 0.5, "NOT FOUND", cex=2)
+								}
+							}
+						}
+						# my.plots[[i]] <- recordPlot()
+					}
+					graphics.off()
+
+					# pdf(file=paste("Unknown_",unkn[l],".pdf", sep=""), onefile=TRUE)
+					# for (my.plot in my.plots) {
+						# replayPlot(my.plot)
+					# }
+					# my.plots
+					# graphics.off()
+
+				}#end  for unkn[l]
+			
+			}
+		
+		}
+	}
+} #end function 
+
+# 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
         }
     }
-    colnames(mat)<-colnames(resGC$PeakTable[,c((which(colnames(resGC$PeakTable)=="rt"|colnames(resGC$PeakTable)=="RI")[length(which(colnames(resGC$PeakTable)=="rt"|colnames(resGC$PeakTable)=="RI"))]+1):dim(resGC$PeakTable)[2])])
-    
-    #debug
-
-    # print(dim(mat))
-    # print(mat[1:3,]) 
-    # write.table(mat, file="myannotationtable.tsv", sep="\t", row.names=FALSE)
-    #correction of annotation matrix due to pcgrp removal by quality check in runGCresult
-    #matrix of correspondance between an@pspectra and filtered pspectra from runGC
-
-    allPCGRPs <-
-        lapply(1:length(resGC$xset),
-            function(i) {
-                an <- resGC$xset[[i]]
-                huhn <- an@pspectra[which(sapply(an@pspectra, length) >=
-                metaSetting(resGC$settings,
-                "DBconstruction.minfeat"))]
-                matCORR<-cbind(1:length(huhn), match(huhn, an@pspectra))
-            })
-
-    if (unkn[1]==""){    
-    #plot EIC and spectra for all unknown for comparative purpose
-   
-
-        par (mar=c(5, 4, 4, 2) + 0.1)
-        for (l in 1:dim(resGC$PeakTable)[1]){ #l=2
-            #recordPlot
-            perpage=3 #if change change layout also!
-            num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
-            my.plots <- vector(num.plots, mode='list')
-            dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",l,".pdf", sep="")) #A4 pdf
-            # par(mfrow=c(perpage,2))
-            layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
-            # layout.show(6)
-            oma.saved <- par("oma")
-            par(oma = rep.int(0, 4))
-            par(oma = oma.saved)
-            o.par <- par(mar = rep.int(0, 4))
-            on.exit(par(o.par))
-            stop=0 #initialize
-            for (i in 1:num.plots) {
-                start=stop+1
-                stop=start+perpage-1 #
-                for (c in start:stop){
-                    if (c <=dim(mat)[2]){
-                            
-                        #get sample name
-                        sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
-
-                        #remove .cdf, .mzXML filepattern
-                        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", 
-                                "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-                        filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), 
-                                collapse = "|")
-                        sampname<-gsub(filepattern, "",sampname)
-                         
-                        title1<-paste("unknown", l,"from",sampname, sep=" ")
-                        an<-resGC$xset[[c]]
-                         
-                        par (mar=c(0, 0, 0, 0) + 0.1)
-                        plot.new()
-                        box()
-                        text(0.5, 0.5, title1, cex=2)
-                        if (!is.na(mat[l,c])){
-                            pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[l,c]),2]
-                            if (pcgrp!=mat[l,c]) print ("pcgrp changed")
-                            par (mar=c(3, 2.5, 3, 1.5) + 0.1)
-                            plotEICs(an, pspec=pcgrp, maxlabel=2)
-                            plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
-                        } else {
-                            plot.new()
-                            box()
-                            text(0.5, 0.5, "NOT FOUND", cex=2)
-                            plot.new()
-                            box()
-                            text(0.5, 0.5, "NOT FOUND", cex=2)
-                        }
-                    }
-                 }
-                # my.plots[[i]] <- recordPlot()
-            }
-            graphics.off()
-
-                # pdf(file=paste("Unknown_",l,".pdf", sep=""), onefile=TRUE)
-                # for (my.plot in my.plots) {
-                    # replayPlot(my.plot)
-                # }
-                # my.plots
-                # graphics.off()
-
-        }#end  for l
-    }#end if unkn=""
-    else{
-        par (mar=c(5, 4, 4, 2) + 0.1)
-        l=unkn
-        if (length(l)==1){
-            #recordPlot
-            perpage=3 #if change change layout also!
-            num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
-            my.plots <- vector(num.plots, mode='list')
-            
-            dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",l,".pdf", sep="")) #A4 pdf
-            # par(mfrow=c(perpage,2))
-            layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
-            # layout.show(6)
-            oma.saved <- par("oma")
-            par(oma = rep.int(0, 4))
-            par(oma = oma.saved)
-            o.par <- par(mar = rep.int(0, 4))
-            on.exit(par(o.par))
-            stop=0 #initialize
-            for (i in 1:num.plots) {
-                start=stop+1
-                stop=start+perpage-1 #
-                for (c in start:stop){
-                    if (c <=dim(mat)[2]){
-                            
-                        #get sample name
-                        sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
-
-                        #remove .cdf, .mzXML filepattern
-                        filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-                        filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
-                        sampname<-gsub(filepattern, "",sampname)
-                         
-                        title1<-paste("unknown", l,"from",sampname, sep=" ")
-                        an<-resGC$xset[[c]]
-                         
-                        par (mar=c(0, 0, 0, 0) + 0.1)
-                        plot.new()
-                        box()
-                        text(0.5, 0.5, title1, cex=2)
-                        if (!is.na(mat[l,c])){
-                            pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[l,c]),2]
-                            if (pcgrp!=mat[l,c]) print ("pcgrp changed")
-                            par (mar=c(3, 2.5, 3, 1.5) + 0.1)
-                            plotEICs(an, pspec=pcgrp, maxlabel=2)
-                            plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
-                        } else {
-                            plot.new()
-                            box()
-                            text(0.5, 0.5, "NOT FOUND", cex=2)
-                            plot.new()
-                            box()
-                            text(0.5, 0.5, "NOT FOUND", cex=2)
-                        }
-                    }
-                }
-                # my.plots[[i]] <- recordPlot()
-            }
-            graphics.off()
-
-            # pdf(file=paste("Unknown_",l,".pdf", sep=""), onefile=TRUE)
-            # for (my.plot in my.plots) {
-                # replayPlot(my.plot)
-            # }
-            # my.plots
-            # graphics.off()
-        } else {
-            par (mar=c(5, 4, 4, 2) + 0.1)
-            for (l in 1:length(unkn)){ #l=2
-                #recordPlot
-                perpage=3 #if change change layout also!
-                num.plots <- ceiling(dim(mat)[2]/perpage) #three pcgroup per page
-                my.plots <- vector(num.plots, mode='list')
-                dev.new(width=21/2.54, height=29.7/2.54, file=paste("Unknown_",unkn[l],".pdf", sep="")) #A4 pdf
-                # par(mfrow=c(perpage,2))
-                layout(matrix(c(1,1,2,3,4,4,5,6,7,7,8,9), 6, 2, byrow = TRUE), widths=rep(c(1,1),perpage), heights=rep(c(1,5),perpage))
-                # layout.show(6)
-                oma.saved <- par("oma")
-                par(oma = rep.int(0, 4))
-                par(oma = oma.saved)
-                o.par <- par(mar = rep.int(0, 4))
-                on.exit(par(o.par))
-                stop=0 #initialize
-                for (i in 1:num.plots) {
-                    start=stop+1
-                    stop=start+perpage-1 #
-                    for (c in start:stop){
-                        if (c <=dim(mat)[2]){
-                        
-                            #get sample name
-                            sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
-
-                            #remove .cdf, .mzXML filepattern
-                            filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
-                            filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
-                            sampname<-gsub(filepattern, "",sampname)
-                             
-                            title1<-paste("unknown",unkn[l],"from",sampname, sep=" ")
-                            an<-resGC$xset[[c]]
-                             
-                            par (mar=c(0, 0, 0, 0) + 0.1)
-                            plot.new()
-                            box()
-                            text(0.5, 0.5, title1, cex=2)
-                            if (!is.na(mat[unkn[l],c])){
-                                pcgrp=allPCGRPs[[c]][which(allPCGRPs[[c]][,1]==mat[unkn[l],c]),2]
-                                if (pcgrp!=mat[unkn[l],c]) print ("pcgrp changed")
-                                par (mar=c(3, 2.5, 3, 1.5) + 0.1)
-                                plotEICs(an, pspec=pcgrp, maxlabel=2)
-                                plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
-                            } else {
-                                plot.new()
-                                box()
-                                text(0.5, 0.5, "NOT FOUND", cex=2)
-                                plot.new()
-                                box()
-                                text(0.5, 0.5, "NOT FOUND", cex=2)
-                            }
-                        }
-                    }
-                    # my.plots[[i]] <- recordPlot()
-                }
-                graphics.off()
-
-                # pdf(file=paste("Unknown_",unkn[l],".pdf", sep=""), onefile=TRUE)
-                # for (my.plot in my.plots) {
-                    # replayPlot(my.plot)
-                # }
-                # my.plots
-                # graphics.off()
-
-            }#end  for unkn[l]
-        
-        }
-    
+    for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
+        listArguments[[argument]]=NULL
     }
-} #end function 
+    return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
+}
 
 
+# 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")
+
+    }
+    return (directory)
+}
+
--- a/metams.r	Wed May 24 07:39:18 2017 -0400
+++ b/metams.r	Thu Jun 08 11:53:35 2017 -0400
@@ -1,7 +1,7 @@
 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
-# metams.r version="2.0"
+# metams.r version="2.1.1"
 #created by Yann GUITTON 
-#use RI options
+#use RI options + add try on plotUnknown add session Info
 
 #Redirect all stdout to the log file
 log_file=file("metams.log", open = "wt")
@@ -16,13 +16,24 @@
     base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
     source(paste(base_dir, fname, sep="/"))
 }
-print("step1")
+# print("step1")
 
 
 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
-print("new version 2.0")
+# print("new version 2.0")
+## constants
+##----------
+
+modNamC <- "metaMS:runGC" ## module name
 
 
+## log file
+##---------
+cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+
+cat("\n1) Parameters:\n")
 print(listArguments)
 
 
@@ -343,8 +354,13 @@
 
 #to do check if no peaks found
 #Quality controls plots but only working in R (don't know why)
-a<-plotUnknowns(resGC=resGC, unkn=unknarg) #use unknparam value
-
+a<-try(plotUnknowns(resGC=resGC, unkn=unknarg)); #use unknparam value
+if(class(a) == "try-error") {
+   pdf("Unknown_Error.pdf")
+	plot.new()
+	text(x=0.5,y=1,pos=1, labels="Error generating EICs\n please use none instead of a vector in plotUnknown")
+   dev.off()
+}
 # create a mergpdf
 
 #test
@@ -370,3 +386,27 @@
 #saving R data in .Rdata file to save the variables used in the present tool
 save.image(paste("runGC","RData",sep="."))
 
+## Closing
+##--------
+
+cat("\nEnd of '", modNamC, "' Galaxy module call: ",
+    as.character(Sys.time()), "\n", sep = "")
+
+cat("\n\n\n============================================================================")
+cat("\nAdditional information about the call:\n")
+# cat("\n1) Parameters:\n")
+# print(cbind(value = argVc))
+
+cat("\n1) Session Info:\n")
+sessioninfo <- sessionInfo()
+cat(sessioninfo$R.version$version.string,"\n")
+cat("Main packages:\n")
+for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+cat("Other loaded packages:\n")
+for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
+
+cat("============================================================================\n")
+
+sink()
+
+rm(list = ls())
\ No newline at end of file
--- a/metams_runGC.xml	Wed May 24 07:39:18 2017 -0400
+++ b/metams_runGC.xml	Thu Jun 08 11:53:35 2017 -0400
@@ -1,4 +1,4 @@
- <tool id="metams_runGC" name="metaMS.runGC" version="2.1">
+ <tool id="metams_runGC" name="metaMS.runGC" version="2.1.1">
        
     <description>GC-MS data preprocessing using metaMS package</description>
     
@@ -57,7 +57,11 @@
             db "NULL"
         #end if
         nSlaves \${GALAXY_SLOTS:-1}
-        unkn "c($unkn)"
+        #if $unkn == "none":
+		   unkn "none"
+		#elif $unkn != "none":
+		   unkn "c($unkn)"
+		#end if
          
     </command>
     
@@ -128,7 +132,7 @@
                     <when value="hide" />
                 </conditional>
                
-                <param name="rtdiff" type="float" value="0.05" label="RT_Diff" help="The allowed RT shift between same molecule in different sample" />
+                <param name="rtdiff" type="float" value="0.05" label="RT_Diff" help="The allowed RT shift in minutes between same molecule in different sample" />
                 <param name="minfeat" type="integer" value="5" label="Min_Features" help="The minimum number of ion in a mass spectra to consider it a molecule" />
                 <param name="simthreshold" type="float" value="0.70" label="similarity_threshold" help="The minimum similarity allowed between peaks mass spectra to be considered as equal" />
                 <param name="minclassfraction" type="float" value="0.5" label="min.class.fract" help="The fraction of samples in which a pseudospectrum is present before it is regarded as an unknown" />
@@ -158,7 +162,7 @@
                 
             </when>
 	     </conditional>
-         <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12  means 1 4 and 12). For all EIC use 0" />
+         <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12  means 1 4 and 12). For all EIC use 0. none for no EIC plot" />
          <conditional name="options_rifilter">
 					<param name="option" type="select" label="Use RI as filter" >
 						<option value="false" selected="true">FALSE</option>
@@ -236,6 +240,7 @@
 Description
 -----------
 metaMS.runGC is a function dedicated to GCMS data processing from converted files to the generation of pseudospectra (compounds) table.
+Current version for metaMS R package: 1.8.0
 
 **Process:** 
 Each of the converted data (cdf, mzML...)  is profiled by a combination of xcms and CAMERA functions. Then all the mass spectra of detected peaks are compared and clustered.
@@ -364,6 +369,11 @@
 Changelog/News
 --------------
 
+**Version 2.1 - 08/06/2017**
+
+- Quality: add sessionInfo logs with packages versions
+- Processing: add RI usage 
+
 **Version 1.1 - 11/07/2016**
 
 - TEST: refactoring to pass planemo test using conda dependencies