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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 # WRAPPER for INTENSITY CHECK
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5 #Script: Script_intensity_check_v1.R
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6 #Xml: xml_intensity_check_v1.xml
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7 #
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8 # V1: Fold and NA
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9 #
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10 # Input: Data Matrix, VariableMetadata, SampleMetadata
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11 # Output: VariableMetadata, Graphics (barplots and boxplots)
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12 #
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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 library(batch) #necessary for parseCommandArgs function
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18 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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19
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20 source_local <- function(...){
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21 argv <- commandArgs(trailingOnly = FALSE)
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22 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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23 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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24 }
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25 #Import the different functions
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26 source_local("Script_intensity_check.R", "RcheckLibrary.R")
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27
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28
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29 if(length(args) < 7){ stop("NOT enough argument !!!") }
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30
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31 class1 <- NULL
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32 if(args$type == "One_class"){
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33 class1 <- args$class1
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34 }
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35
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36 #print args
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37 cat("\n-------------------------------\nIntensity Check parameters:\n\n")
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38 print(args)
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39 cat("--------------------------------\n")
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40
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41
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42 intens_check(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, args$type,
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43 args$class_col, class1, args$variableMetadata_out, args$graphs_out)
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44
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45 sessionInfo()
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46 cat("--------------------------------\n")
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47
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48 #delete the parameters to avoid the passage to the next tool in .RData image
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49 rm(args)
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