--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RnBeadsGalaxy.R	Sat Apr 20 07:14:22 2013 -0400
@@ -0,0 +1,173 @@
+msg.file<-file("RnBeads.messages.out")
+sink(file=open(msg.file, "w"))
+
+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"
+	files<-strsplit(opts[["idat-files"]], "\t")[[1]]
+	idat.dir<-mkdir(file.path(opts[["report-dir"]], "idats"))
+	file.copy(as.list(files), idat.dir)
+	data.source<-list()
+	data.source[["idat.dir"]]<-idat.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"]]=="beds"){
+
+	data.type<-"idat.dir"
+	files<-strsplit(opts[["bed-files"]], "\t")[[1]]
+	bed.dir<-mkdir(file.path(opts[["report-dir"]], "beds"))
+	file.copy(as.list(files), bed.dir)
+	data.source<-list()
+	data.source[["bed.dir"]]<-bed.dir
+	data.source[["sample.sheet"]]<-opts[["pheno"]]
+
+}
+
+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)))	
+		})
+
+#report.out.dir<-sprintf("%s_rnbReport", tempdir())
+report.out.dir<-opts[["report-dir"]]
+suppressMessages(suppressWarnings(rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type)))
+
+#file.symlink(paste(report.out.dir, "index.html", sep="/"), opts[["output-file"]]) 
+
+outfile<-file(opts[["output-file"]],open="w")
+cat(sprintf("<html>\n<body>\n<a href=\"index.html\">RnBeads report</a>\n</body>\n</html>",report.out.dir),file=outfile)
+close(outfile)
+
+sink(file=NULL)
+flush(msg.file)
+close(msg.file)
+