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1 # Start_GenometriCorr.R
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2
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3 ###################################################
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4 # #
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5 # command-line interface to GenometriCorr #
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6 # functions, for use with Galaxy. #
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7 # #
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8 ###################################################
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9
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10 capture.output <- function (result, pdffile, output_options)
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11 {
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12 if(output_options != "stats")
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13 {
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14 pdf(file=pdffile, width=10, height=19, paper="special")
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15
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16 if (output_options != "vis") #need to do a plot
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17 {
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18 mymat <- matrix(ncol=3, nrow=4)
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19 mymat[1,1] <- 1
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20 mymat[1,2] <- 2
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21 mymat[1,3] <- 3
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22 mymat[2,1] <- 4
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23 mymat[2,2] <- 5
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24 mymat[2,3] <- 6
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25 mymat[3,1] <- 7
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26 mymat[3,2] <- 8
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27 mymat[3,3] <- 9
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28 mymat[4,1] <- 10
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29 mymat[4,2] <- 11
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30 mymat[4,3] <- 12
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31
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32 layout(mymat, heights=c(0.2,0.2,0.2,0.2))
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33 plot(result, pdffile, make.new=FALSE)
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34 }
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35 if (output_options != "plot") #need to do the bigger graphic
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36 {
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37 mymat <- matrix(ncol=2, nrow=8)
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38 mymat[1,1] <- 2
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39 mymat[1,2] <- 3
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40 mymat[2,1] <- 4
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41 mymat[2,2] <- 4
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42 mymat[3,1] <- 1
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43 mymat[3,2] <- 1
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44 mymat[4,1] <- 5
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45 mymat[4,2] <- 6
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46 mymat[5,1] <- 7
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47 mymat[5,2] <- 7
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48 mymat[6,1] <- 8
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49 mymat[6,2] <- 9
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50 mymat[7,1] <- 10
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51 mymat[7,2] <- 10
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52 mymat[8,1] <- 11
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53 mymat[8,2] <- 12
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54 layoutresults <- 3
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55
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56 layout(mymat, heights=c(0.05,0.05,0.15,0.15,0.15,0.15,0.15,0.15))
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57 visualize(result, pdffile, make.new=FALSE)
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58 }
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59 dev.off()
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60 }
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61
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62 if (output_options == "stats")
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63 {
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64 show(result)
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65 }
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66 }
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67
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68
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69
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70 # Reads the command line arguments
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71 args <- commandArgs(trailingOnly=T)
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72
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73 suppressPackageStartupMessages(library('GenometriCorr', warn.conflicts=F, verbose=F))
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74 suppressPackageStartupMessages(library('graphics', warn.conflicts=F, verbose=F))
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75 suppressPackageStartupMessages(library('gdata', warn.conflicts=F, verbose=F))
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76 suppressPackageStartupMessages(library('gplots', warn.conflicts=F, verbose=F))
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77 suppressPackageStartupMessages(library('gtools', warn.conflicts=F, verbose=F))
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78 suppressPackageStartupMessages(library('caTools', warn.conflicts=F, verbose=F))
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79 suppressPackageStartupMessages(library('grid', warn.conflicts=F, verbose=F))
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80
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81
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82
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83 # Variables
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84 query_file <- ""
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85 reference_file <- ""
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86 config_file <- ""
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87 output_options <- ""
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88
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89 # Parse the command line arguments
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90
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91 config_file <- args[1]
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92 query_file <- as.character(args[2])
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93 reference_file <- as.character(args[3])
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94 output_options <- args[4]
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95 pdffile <- args[5]
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96
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97 conf<-new("GenometriCorrConfig",config_file)
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98
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99 print('OK')
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100
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101 result<-suppressWarnings(suppressPackageStartupMessages(GenometriCorr:::run.config(conf,query=query_file,reference=reference_file)))
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102 print('OK2')
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103
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104 hideoutput <- capture.output(result, pdffile=args[5], output_options)
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105
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