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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
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2
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3
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4 #############################################################################
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5 # WRAPPER for INTENSITY CHECK #
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6 # #
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7 #Script: Script_intensity_check.R #
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8 #Xml: xml_intensity_check.xml #
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9 # #
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10 # #
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11 # Input: Data Matrix, VariableMetadata, SampleMetadata #
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12 # Output: VariableMetadata, Graphics #
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13 # #
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14 # #
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15 #############################################################################
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16
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17
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18 library(batch) #necessary for parseCommandArgs function
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19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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20
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21 source_local <- function(...){
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22 argv <- commandArgs(trailingOnly = FALSE)
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23 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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24 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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25 }
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26 #Import the different functions
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27 source_local("Script_intensity_check.R", "RcheckLibrary.R")
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28
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29
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30 if(length(args) < 7){ stop("NOT enough argument !!!") }
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31
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32 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
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33 '\n\n--------------------------------------------------------------------',
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34 '\nIntensity Check parameters:\n\n')
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35 print(args)
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36 cat('--------------------------------------------------------------------\n\n')
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37
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38 class_col <- NULL
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39 test_fold <- NULL
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40 class1 <- NULL
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41 fold_frac <- NULL
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42 logarithm <- NULL
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43 if(args$method == "each_class"){
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44 class_col <- args$class_col
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45 test_fold <- args$test_fold
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46 if(args$test_fold == "Yes"){
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47 logarithm <- args$logarithm
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48 }
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49 }
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50 if(args$method == "one_class"){
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51 class_col <- args$class_col
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52 class1 <- args$class1
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53 test_fold <- args$test_fold
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54 if(args$test_fold == "Yes"){
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55 fold_frac <- args$fold_frac
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56 logarithm <- args$logarithm
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57 }
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58 }
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59
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60 err_no_option <- NULL
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61
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62 if(((args$method == "no_class")&&(args$chosen_stat == "None"))||
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63 ((args$method != "no_class") && (args$chosen_stat == "None") && (test_fold == "No"))){
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64 err_no_option<- "You did not select any computational option. Program can not be executed."
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65 stop("\n- - - - - - - - -\n",err_no_option,"\n- - - - - - - - -\n")
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66 }
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67
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68
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69 if(is.null(err_no_option)){
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70
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71 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$method, args$chosen_stat,
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72 class_col, test_fold, class1, fold_frac, logarithm, args$variableMetadata_out, args$graphs_out)
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73 }
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74
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75
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76 cat('\n--------------------------------------------------------------------',
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77 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
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78 sessionInfo()
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79 cat('--------------------------------------------------------------------\n',
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80 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
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81
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82
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83 #delete the parameters to avoid the passage to the next tool in .RData image
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84 rm(args)
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