Mercurial > repos > mmonsoor > probmetab

annotate probmetab.r @ 0:e13ec2c3fabe draft

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planemo upload commit 25fd6a739741295e3f434e0be0286dee61e06825
author mmonsoor
date Mon, 04 Jul 2016 04:29:25 -0400
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children abcfa1648b66
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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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5
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6 # ----- LOG -----
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7 log_file=file("probmetab.log", 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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18
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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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24 cat("\n\n")
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25 # ----- ARGUMENTS -----
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26 cat("\tARGUMENTS INFO\n")
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27 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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28 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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31
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32 # ----- PROCESSING INFILE -----
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33 cat("\tINFILE PROCESSING INFO\n")
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34
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35 # ----- INFILE PROCESSING -----
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36
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37 if(listArguments[["mode_acquisition"]]=="one") {
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38 load(listArguments[["xa"]])
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39
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40 if (!is.null(listArguments[["zipfile"]])){
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41 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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42 }
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43
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44 #Unzip the chromatograms file for plotting EIC pour the HTML file
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45 if(exists("zipfile"))
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46 {
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47 if (zipfile!=""){
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48 directory=unzip(zipfile)
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49 }
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50 }
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51 if (!exists("xa")) {
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52 xa=xsAnnotate_object
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53 }
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54 source_local("lib.r")
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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 load(listArguments[["image_pos"]])
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59
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60 if (!is.null(listArguments[["zipfile"]])){
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61 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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62 }
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63
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64 #Unzip the chromatograms file for plotting EIC pour the HTML file
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65 if(exists("zipfile")) {
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66 if (zipfile!=""){
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67 directory=unzip(zipfile)
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68 }
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69 }
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70 if (!exists("xa")) {
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71 xa=xsAnnotate_object
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72 }
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73 xaP=xa
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74 source_local("lib.r")
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75 if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa)
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76 else variableMetadataP=variableMetadata
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77
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78
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79 load(listArguments[["image_neg"]])
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80
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81 if (!is.null(listArguments[["zipfile"]])){
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82 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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83 }
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84
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85 #Unzip the chromatograms file for plotting EIC pour the HTML file
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86 if(exists("zipfile")) {
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87
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88 if (zipfile!=""){
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89 directory=unzip(zipfile)
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90 }
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91 }
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92 if (!exists("xa")) {
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93 xa=xsAnnotate_object
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94 }
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95 xaN=xa
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96 source_local("lib.r")
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97
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98 if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa)
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99 else variableMetadataN=variableMetadata
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100 }
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101
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102 #Import the different functions
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103 source_local("lib.r")
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104 source_local("export.class.table-color-graph.R")
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105
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106 # ----- PROCESSING INFO -----
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107 cat("\tMAIN PROCESSING INFO\n")
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108
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109 if(listArguments[["mode_acquisition"]]=="one") {
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110 results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
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111 } else if(listArguments[["inputs_mode"]]=="two"){
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112 results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
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113 }
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114 #delete the parameters to avoid the passage to the next tool in .RData image
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115 #rm(listArguments)
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116 cat("\tDONE\n")
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117 #saving R data in .Rdata file to save the variables used in the present tool
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118 #save.image(paste("probmetab","RData",sep="."))
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119