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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 filter_script.R (GENERIC FILTERS) #
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5 # #
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6 # Author: Melanie PETERA based on Marion LANDI's filters' wrapper #
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7 # User: Galaxy #
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8 # Original data: used with filter_script.R #
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9 # Starting date: 04-09-2014 #
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10 # V-1: Restriction of old filter wrapper to Filter according to factors #
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11 # V-1.1: Modification to allow the choice of meta-data table for filtering #
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12 # V-2: Addition of numerical filter #
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13 # V-2.5: -h option + additional information in stdout #
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14 # #
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15 # #
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16 # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
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17 # Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
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18 # #
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19 ################################################################################################
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20
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21
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22 library(batch) #necessary for parseCommandArgs function
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3
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23
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24 # Constants
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25 argv <- commandArgs(trailingOnly = FALSE)
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26 script.path <- sub("--file=","",argv[grep("--file=",argv)])
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27 prog.name <- basename(script.path)
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28
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29 # Help
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30 if (length(grep('-h', argv)) >0) {
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31 cat("Usage:", prog.name,
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32 "dataMatrix_in myDataMatrix.tsv",
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33 "sampleMetadata_in mySampleMetadata.tsv",
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34 "variableMetadata_in myVariableMetadata.tsv",
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35 "...",
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36 "\n")
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37 quit(status = 0)
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38 }
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39
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40 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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41
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42 source_local <- function(...){
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43 argv <- commandArgs(trailingOnly = FALSE)
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44 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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45 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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46 }
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47 #Import the different functions
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48 source_local("filter_script.R","RcheckLibrary.R","miniTools.R")
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49
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50
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51 if(length(args) < 8){ stop("NOT enough argument !!!") }
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52
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53
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54 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
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55 '\n\n--------------------------------------------------------------------',
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56 '\nParameters used in "Generic Filter":\n\n')
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57 print(args)
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58 cat('--------------------------------------------------------------------\n\n')
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59
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60
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61 list_num <- NULL
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62 if(!is.null(args$parm_col)){
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63 for( i in which(names(args)=="num_file") ){
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64 if(args[[i+2]] %in% c("lower","upper")){
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65 list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]])))
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66 }
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67 if(args[[i+2]] %in% c("between","extremity")){
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68 list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]],args[[i+4]])))
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69 }
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70 }
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71 }
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72
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73 list_fact <- NULL
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74 if(!is.null(args$factor_col)){
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75 for( i in which(names(args)=="qual_file") ){
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76 list_fact <- c(list_fact, list(c(args[[i+1]], args[[i+2]], args[[i]])))
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77 }
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78 }
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79
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80 filters(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in,
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81 args$Numeric, list_num, args$Factors, list_fact,
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82 args$dataMatrix_out, args$sampleMetadata_out, args$variableMetadata_out)
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83
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84 #filters(ion.file.in, meta.samp.file.in, meta.ion.file.in,
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85 # NUM, ls.num, FACT, ls.fact,
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86 # ion.file.out, meta.samp.file.out, meta.ion.file.out)
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87
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88
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89 cat('\n--------------------------------------------------------------------',
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90 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
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91 sessionInfo()
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92 cat('--------------------------------------------------------------------\n',
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93 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
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94
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95
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96 #delete the parameters to avoid the passage to the next tool in .RData image
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97 rm(args)
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