--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/Start_GenometriCorr.R	Fri Mar 09 20:01:43 2012 -0500
@@ -0,0 +1,105 @@
+# Start_GenometriCorr.R
+
+###################################################
+#                                                 #
+#  command-line interface to GenometriCorr        #
+#  functions, for use with Galaxy.                #
+#                                                 #
+###################################################
+
+capture.output <- function (result, pdffile, output_options)
+{
+   if(output_options != "stats")
+   {
+      pdf(file=pdffile, width=10, height=19, paper="special")
+   
+      if (output_options != "vis")   #need to do a plot
+      {
+         mymat <- matrix(ncol=3, nrow=4)
+         mymat[1,1] <- 1
+         mymat[1,2] <- 2
+         mymat[1,3] <- 3
+         mymat[2,1] <- 4
+         mymat[2,2] <- 5
+         mymat[2,3] <- 6
+         mymat[3,1] <- 7
+         mymat[3,2] <- 8
+         mymat[3,3] <- 9
+         mymat[4,1] <- 10
+         mymat[4,2] <- 11
+         mymat[4,3] <- 12
+       
+         layout(mymat, heights=c(0.2,0.2,0.2,0.2))
+         plot(result, pdffile, make.new=FALSE)
+      }
+      if (output_options != "plot")  #need to do the bigger graphic
+      {
+         mymat <- matrix(ncol=2, nrow=8)
+         mymat[1,1] <- 2
+         mymat[1,2] <- 3
+         mymat[2,1] <- 4
+         mymat[2,2] <- 4
+         mymat[3,1] <- 1
+         mymat[3,2] <- 1
+         mymat[4,1] <- 5
+         mymat[4,2] <- 6
+         mymat[5,1] <- 7
+         mymat[5,2] <- 7
+         mymat[6,1] <- 8
+         mymat[6,2] <- 9 
+         mymat[7,1] <- 10
+         mymat[7,2] <- 10
+         mymat[8,1] <- 11
+         mymat[8,2] <- 12
+         layoutresults <- 3
+         
+         layout(mymat, heights=c(0.05,0.05,0.15,0.15,0.15,0.15,0.15,0.15))
+         visualize(result, pdffile, make.new=FALSE) 
+      }
+      dev.off()
+   } 
+   
+   if (output_options == "stats")
+   {
+      show(result)
+   }
+}
+
+
+
+# Reads the command line arguments
+args <- commandArgs(trailingOnly=T)
+
+suppressPackageStartupMessages(library('GenometriCorr',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('graphics',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('gdata',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('gplots',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('gtools',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('caTools',  warn.conflicts=F, verbose=F))
+suppressPackageStartupMessages(library('grid',  warn.conflicts=F, verbose=F))
+
+
+
+# Variables
+query_file <- ""
+reference_file <- ""
+config_file <- ""
+output_options <- ""
+
+# Parse the command line arguments
+
+config_file <- args[1]
+query_file <- as.character(args[2])
+reference_file <- as.character(args[3])
+output_options <- args[4]
+pdffile <- args[5]
+
+conf<-new("GenometriCorrConfig",config_file)
+
+print('OK')
+
+result<-suppressWarnings(suppressPackageStartupMessages(GenometriCorr:::run.config(conf,query=query_file,reference=reference_file)))
+print('OK2')
+
+hideoutput <- capture.output(result, pdffile=args[5], output_options)
+