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planemo upload commit 858f2560108824c0c4d6e9f700d1690308bb13ad
author lecorguille
date Tue, 24 May 2016 11:17:59 -0400
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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("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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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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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 # ----- PROCESSING INFILE -----
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32 cat("\tINFILE PROCESSING INFO\n")
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33
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34 # ----- INFILE PROCESSING -----
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35
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36 if(listArguments[["mode_acquisition"]]=="one") {
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37 load(listArguments[["xa"]])
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38 #Unzip the chromatograms file for plotting EIC pour the HTML file
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39 if(exists("zipfile"))
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40 {
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41 if (zipfile!=""){
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42 directory=unzip(zipfile)
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43 }
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44 }
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45 if (!exists("xa")) {
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46 xa=xsAnnotate_object
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47 }
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48 source_local("lib.r")
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49 if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
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50
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51 } else if(listArguments[["inputs_mode"]]=="two"){
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52 load(listArguments[["image_pos"]])
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53 #Unzip the chromatograms file for plotting EIC pour the HTML file
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54 if(exists("zipfile")) {
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55 if (zipfile!=""){
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56 directory=unzip(zipfile)
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57 }
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58 }
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59 if (!exists("xa")) {
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60 xa=xsAnnotate_object
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61 }
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62 xaP=xa
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63 source_local("lib.r")
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64 if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa)
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65 else variableMetadataP=variableMetadata
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66
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67
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68 load(listArguments[["image_neg"]])
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69 #Unzip the chromatograms file for plotting EIC pour the HTML file
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70 if(exists("zipfile")) {
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71
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72 if (zipfile!=""){
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73 directory=unzip(zipfile)
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74 }
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75 }
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76 if (!exists("xa")) {
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77 xa=xsAnnotate_object
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78 }
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79 xaN=xa
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80 source_local("lib.r")
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81
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82 if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa)
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83 else variableMetadataN=variableMetadata
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84 }
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85
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86 print(directory)
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87 print(dir(directory))
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88
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89 #Import the different functions
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90 source_local("lib.r")
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91 source_local("export.class.table-color-graph.R")
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92
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93 # ----- PROCESSING INFO -----
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94 cat("\tMAIN PROCESSING INFO\n")
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95
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96 if(listArguments[["mode_acquisition"]]=="one") {
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97 results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
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98 } else if(listArguments[["inputs_mode"]]=="two"){
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99 results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
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100 }
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101 #delete the parameters to avoid the passage to the next tool in .RData image
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102 #rm(listArguments)
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103 cat("\tDONE\n")
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104 #saving R data in .Rdata file to save the variables used in the present tool
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105 #save.image(paste("probmetab","RData",sep="."))
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106