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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
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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 (barplots and boxplots) #
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13 # #
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14 # #
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15 #############################################################################
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16
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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) < 8){ stop("NOT enough argument !!!") }
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31
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32
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33 class1 <- NULL
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34 fold_frac <- NULL
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35 if(args$type == "One_class"){
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36 class1 <- args$class1
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37 fold_frac <- args$fold_frac
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38 }
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39
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40
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41 #print args
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42 cat("\n-------------------------------\nIntensity Check parameters:\n\n")
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43 print(args)
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44 cat("--------------------------------\n")
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45
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46
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47 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$class_col, args$type,
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48 class1, fold_frac, args$logarithm, args$variableMetadata_out, args$graphs_out)
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49
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50 sessionInfo()
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51 cat("--------------------------------\n")
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52
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53 #delete the parameters to avoid the passage to the next tool in .RData image
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54 rm(args)
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