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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 tablemerge_script.R (TABLE MERGE) #
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5 # #
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6 # Author: Melanie PETERA #
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7 # User: Galaxy #
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8 # Original data: used with tablemerge_script.R #
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9 # Starting date: 11-05-2015 #
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10 # V-1: First version of wrapper #
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11 # V-2: Addition of prints about input parameters and job info #
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12 # #
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13 # #
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14 # Input files: dataMatrix ; Metadata file #
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15 # Output files: dataMatrix ; Metadata file #
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16 # #
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17 ################################################################################################
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18
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19
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20 library(batch) #necessary for parseCommandArgs function
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21 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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22
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23 source_local <- function(...){
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24 argv <- commandArgs(trailingOnly = FALSE)
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25 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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26 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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27 }
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28 #Import the different functions
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29 source_local("tablemerge_script.R","RcheckLibrary.R","miniTools.R")
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30
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31
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32 if(length(args) < 4){ stop("NOT enough argument !!!") }
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33
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34
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35 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
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36 '\n\n--------------------------------------------------------------------',
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37 '\nParameters used in "Table Merge":\n\n')
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38 print(args)
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39 cat('--------------------------------------------------------------------\n\n')
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40
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41
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42 tab.merge(args$dataMatrix_in, args$Metadata_in, args$metatype, args$combined_out)
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43
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44
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45 cat('\n--------------------------------------------------------------------',
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46 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
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47 sessionInfo()
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48 cat('--------------------------------------------------------------------\n',
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49 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
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50
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51
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52 #delete the parameters to avoid the passage to the next tool in .RData image
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53 rm(args)
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