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annotate probmetab.r @ 9:fe21deb6b625 draft

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planemo upload commit 4119e0f73e028bf420e5bdec2d95a4621ebbbcaf
author lecorguille
date Fri, 07 Apr 2017 07:56:16 -0400
parents 1dd90aa7815d
children
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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2 # probmetab.r version="1.0.0"
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3 # Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
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6 # ----- LOG -----
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7 log_file=file("log.txt", open = "wt")
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8 sink(log_file)
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9 sink(log_file, type = "out")
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10
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11 # ----- PACKAGE -----
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12 cat("\tPACKAGE INFO\n")
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13 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
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14 for(p in pkgs) {
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15 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
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16 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
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17 }
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19 source_local <- function(fname){
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20 argv <- commandArgs(trailingOnly = FALSE)
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21 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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22 source(paste(base_dir, fname, sep="/"))
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23 }
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25 options(bitmapType='cairo')
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26
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27 cat("\n\n")
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29
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30 # ----- ARGUMENTS -----
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31 cat("\tARGUMENTS INFO\n")
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32 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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33 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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34
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36
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37 # ----- PROCESSING INFILE -----
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38 cat("\tINFILE PROCESSING INFO\n")
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39
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40 # ----- INFILE PROCESSING -----
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41
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42 if(listArguments[["mode_acquisition"]]=="one") {
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43 load(listArguments[["image"]])
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44 cat("\t\tXA OBJECT INFO\n")
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45 print(xa)
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47 source_local("lib.r")
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48 if (!exists("zipfile")) zipfile=NULL
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49 if (!exists("singlefile")) singlefile=NULL
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50 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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51 zipfile = rawFilePath$zipfile
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52 singlefile = rawFilePath$singlefile
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53 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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54
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55 if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
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56
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57 } else if(listArguments[["inputs_mode"]]=="two"){
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58
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59 # POSITIVE
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60 load(listArguments[["image_pos"]])
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61
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62 if (!exists("xa")) xaP=xsAnnotate_object
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63 else xaP=xa
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64 cat("\t\tXA-POSITIVE OBJECT INFO\n")
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65 print(xaP)
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66
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67 if (!exists("variableMetadata")) variableMetadataP = getVariableMetadata(xa)
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68 else variableMetadataP = variableMetadata
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69
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70 source_local("lib.r")
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71 if (!exists("zipfile")) zipfile=NULL
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72 if (!exists("singlefile")) singlefile=NULL
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73 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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74 zipfilePos = rawFilePath$zipfile
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75 singlefilePos = rawFilePath$singlefile
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76 retrieveRawfileInTheWorkingDirectory(singlefilePos, zipfilePos)
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77
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78 # NEGATIVE
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79 load(listArguments[["image_neg"]])
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80
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81 if (!exists("xa")) xaN=xsAnnotate_object
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82 else xaN=xa
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83 cat("\t\tXA-NEGATIVE OBJECT INFO\n")
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84 print(xaP)
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85
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86 if (!exists("variableMetadata")) variableMetadataN = getVariableMetadata(xa)
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87 else variableMetadataN = variableMetadata
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88
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89 source_local("lib.r")
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90 if (!exists("zipfile")) zipfile=NULL
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91 if (!exists("singlefile")) singlefile=NULL
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92 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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93 zipfileNeg = rawFilePath$zipfile
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94 singlefileNeg = rawFilePath$singlefile
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95 retrieveRawfileInTheWorkingDirectory(singlefileNeg, zipfileNeg)
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96 }
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97
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98 #Import the different functions
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99 source_local("lib.r")
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100 source_local("export.class.table-color-graph.R")
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101
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102 # ----- PROCESSING INFO -----
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103 cat("\tMAIN PROCESSING INFO\n")
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104
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105 if(listArguments[["mode_acquisition"]]=="one") {
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106 results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
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107 } else if(listArguments[["inputs_mode"]]=="two"){
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108 results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
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109 }
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110 #delete the parameters to avoid the passage to the next tool in .RData image
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111 #rm(listArguments)
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112 cat("\tDONE\n")
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113 #saving R data in .Rdata file to save the variables used in the present tool
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114 #save.image(paste("probmetab","RData",sep="."))