--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RnBeadsGalaxy.R	Fri Jul 05 15:14:26 2013 -0400
@@ -0,0 +1,206 @@
+#msg.file<-file("RnBeads.messages.out", open="w")
+#sink(file=msg.file)
+
+
+## add the RnBeads dependencies if we are on a cloud share-instance
+if("Rsitelibrary" %in% list.files("/mnt")){
+	
+	.libPaths("/mnt/Rsitelibrary")
+	
+}
+
+suppressWarnings(suppressPackageStartupMessages(library(RnBeads)))
+suppressWarnings(suppressPackageStartupMessages(library(getopt)))
+
+#all.opts<-names(rnb.options())
+opt.class<-RnBeads:::OPTION.TYPES[-28]
+all.opts<-names(opt.class)
+#all.opts<-paste("--", all.opts, sep="")
+#all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE)
+all.opts<-gsub("\\.","-", all.opts)
+#opt.class<-sapply(rnb.options(), class)
+
+rnb.opt.spec<-data.frame(
+		Long=all.opts, 
+		Short=as.character(1:length(all.opts)), 
+		Mask=c(1,2)[as.integer((opt.class=="logical"))+1], 
+		Type=opt.class)
+
+### automated xml file preparation
+xml.strings<-apply(rnb.opt.spec,1, function(row){
+			
+			opt.lab<-gsub("-", ".", row[1])
+			opt.def.val<-rnb.getOption(opt.lab)
+			opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
+			tf.opt<-"\t\t\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>"
+			opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ")
+			if(row[4]=="logical"){
+				opt.type<-'select'
+				if(!is.null(opt.def.val) && opt.def.val)
+					opt.def.val<-"1" else
+					opt.def.val<-"0"
+				string<-sprintf("\t\t<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\">\n%s\n\t\t</param>\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt)
+			}else{
+				opt.type<-'text'
+				if(!is.null(opt.def.val) && opt.def.val!="")
+					opt.def.val<-paste(opt.def.val, collapse=",") else
+					opt.def.val<-""
+				string<-sprintf("\t\t<param name=\"%s\" type=\"%s\"  label=\"%s\" value=\"%s\"/>\n", opt.name, opt.type, opt.lab, opt.def.val)
+			}
+			string
+		})
+
+cat(xml.strings, sep="", file="automated.settings.xml.txt")
+
+opt.def.strings<-apply(rnb.opt.spec,1, function(row){
+			
+			opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
+			opt.long<-row[1]
+			opt.short<-row[2]
+			
+			if(row[4]=="logical"){
+				def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)		
+			}else{
+				def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
+			}
+			def.string
+			
+		})
+cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
+
+
+rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
+rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
+rnb.opt.spec<-rbind(data.frame(
+				Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"),
+				Short=c("d","s","a","i","f","g","e","b","p","r","o"),
+				Mask=c(1,2,2,2,2,2,2,2,2,1,1),
+				Type=c("character","character","character","character","character","character","character","character","character","character", "character")),
+				rnb.opt.spec)
+		
+opts<-getopt(as.matrix(rnb.opt.spec))
+#opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2"))
+print(opts)
+
+if(opts[["data-type"]]=="idatDir"){
+   
+	data.source<-list()
+	data.type<-"idat.dir"
+	data.source[["idat.dir"]]<-opts[["idat-dir"]]
+	data.source[["sample.sheet"]]<-opts[["pheno"]]
+   
+}else if(opts[["data-type"]]=="idatFiles"){
+	
+	data.type<-"idat.dir"
+	file.string<-gsub(" ","", opts[["idat-files"]])
+	files<-strsplit(file.string, ",")[[1]]
+	files<-files[files!=""]
+	bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
+	dir.create(bed.dir)
+	file.copy(files, bed.dir)
+	for(dat.file in list.files(bed.dir, full.names = TRUE)){
+		file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
+	}
+	data.source<-list()
+	data.source[["bed.dir"]]<-bed.dir
+	data.source[["sample.sheet"]]<-opts[["pheno"]]
+	
+	
+}else if(opts[["data-type"]]=="GS.report"){
+
+	data.type<-"GS.report"
+	data.source<-opts[["gs-report"]]
+	
+}else if(opts[["data-type"]]=="GEO"){
+	
+	data.type<-"GEO"
+	data.source<-opts[["geo-series"]]
+	
+}else if(opts[["data-type"]]=="data.files"){
+	
+	data.type<-"GEO"
+	data.source<-opts[["geo-series"]]
+	
+}else if(opts[["data-type"]]=="data.files"){
+	
+	data.type<-"data.files"
+	data.source<-c(opts[["pheno"]], opts[["betas"]])
+	if(!is.null(opts[["pvals"]]))
+		data.source<-c(data.source, opts[["pvals"]])
+		
+}else if(opts[["data-type"]]=="bed.dir"){
+
+	data.type<-"bed.dir"
+	file.string<-gsub(" ","", opts[["bed-files"]])
+	files<-strsplit(file.string, ",")[[1]]
+	files<-files[files!=""]
+	bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
+	dir.create(bed.dir)
+	file.copy(files, bed.dir)
+	for(dat.file in list.files(bed.dir, full.names = TRUE)){
+		file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
+	}
+	data.source<-list()
+	data.source[["bed.dir"]]<-bed.dir
+	
+	logger.start(fname="NA")
+	sample.sheet<-rnb.read.annotation(opts[["pheno"]])
+	logger.close()
+	if(length(files) < nrow(sample.sheet))
+		stop("Not all bed files are present")
+	
+	cn<-colnames(sample.sheet)
+	dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)])
+	sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files))
+	colnames(sample.sheet)<-c(cn, "BED_files")
+	data.source[["sample.sheet"]]<-sample.sheet
+}
+
+if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied
+	
+	dump<-sapply(names(opt.class), function(on){
+		getoptname<-gsub("-", "\\.","-",on)
+		if(getoptname %in% names(opts)){
+			if(opt.class[on]=="logical"){
+				ov<-TRUE
+			}else if(opt.class %in% c("character","character.vector")){
+				ov<-opts[[getoptname]]
+				ov<-gsub("\"", "", ov)
+				if(opt.class=="character.vector"){
+					ov<-as.character(strsplit(ov,","))
+				}
+				
+			}else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){
+				ov<-opts[[getoptname]]
+				ov<-gsub("\"", "", ov)
+				if(opt.class %in% c("integer.vector","numeric.vector")){
+					ov<-as.character(strsplit(ov,","))
+				}
+			}
+			eval(parse(text=sprintf("rnb.options(%s=ov)",on)))
+		}
+	})
+	
+	logical.opts<-names(opt.class[opt.class=="logical"])
+	logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))]
+	
+	
+	dump<-sapply(logical.opts.false, function(on){
+				eval(parse(text=sprintf("rnb.options(%s=FALSE)",on)))	
+			})
+}
+
+print(rnb.options())
+
+#report.out.dir<-sprintf("%s_rnbReport", tempdir())
+report.out.dir<-opts[["report-dir"]]
+print("Starting RnBeads with the following inputs:")
+print(data.source)
+print(report.out.dir)
+print(data.type)
+rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type)
+
+
+#sink(file=NULL)
+#flush(msg.file)
+#close(msg.file)
\ No newline at end of file