--- a/Start_GenometriCorr.R	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-# 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)
-