# 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)