Mercurial > repos > lecorguille > ipo

annotate ipo4retgroup.r @ 6:03fdfbd914ab draft

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planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
author lecorguille
date Thu, 30 Mar 2017 11:27:09 -0400
parents
children 80de755766a8
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1 #!/usr/bin/env Rscript
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2 #Authors Gildas Le Corguille and Yann Guitton
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5 # ----- LOG FILE -----
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6 log_file=file("log.txt", open = "wt")
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7 sink(log_file)
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8 sink(log_file, type = "output")
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11 # ----- PACKAGE -----
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12 options(bitmapType='cairo')
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13 cat("\tPACKAGE INFO\n")
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14 #pkgs=c("xcms","batch")
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15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch")
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16 for(pkg in pkgs) {
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17 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
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18 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
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19 }
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20 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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21 cat("\n\n");
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24 # ----- ARGUMENTS -----
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25 cat("\tARGUMENTS INFO\n")
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26 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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27 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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28
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29 cat("\n\n");
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32 # ----- ARGUMENTS PROCESSING -----
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33 cat("\tINFILE PROCESSING INFO\n")
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34
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35 #image is an .RData file necessary to use xset variable given by previous tools
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36 if (!is.null(listArguments[["image"]])){
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37 load(listArguments[["image"]]); listArguments[["image"]]=NULL
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38 }
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39
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40 #Import the different functions
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41 source_local("lib.r")
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42
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43 cat("\n\n")
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44
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45 #Import the different functions
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46
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47 # ----- PROCESSING INFILE -----
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48 cat("\tARGUMENTS PROCESSING INFO\n")
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51 parametersOutput = "parametersOutput.tsv"
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52 if (!is.null(listArguments[["parametersOutput"]])){
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53 parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL
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54 }
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55
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56 samplebyclass = 2
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57 if (!is.null(listArguments[["samplebyclass"]])){
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58 samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL
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59 }
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60
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61 #necessary to unzip .zip file uploaded to Galaxy
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62 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
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64
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65 if (!is.null(listArguments[["zipfile"]])){
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66 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
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67 }
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69
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70 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
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71 singlefile_galaxyPath = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
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72 singlefile_sampleName = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
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73 }
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74
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75 # single file case
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76 #@TODO: need to be refactoring
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77 if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
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78
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79 cwd=getwd()
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80 dir.create("raw")
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81 setwd("raw")
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82
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83 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPath))) {
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84 if(!file.exists(singlefile_galaxyPath[singlefile_galaxyPath_i])){
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85 error_message=paste("Cannot access the sample:",singlefile_sampleName[singlefile_galaxyPath_i],"located:",singlefile_galaxyPath[singlefile_galaxyPath_i],". Please, contact your administrator ... if you have one!")
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86 print(error_message); stop(error_message)
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87 }
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88 file.symlink(singlefile_galaxyPath[singlefile_galaxyPath_i],singlefile_sampleName[singlefile_galaxyPath_i])
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89 }
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90
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91 setwd(cwd)
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92
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93 directory = "raw"
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94
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95 }
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96
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97 # We unzip automatically the chromatograms from the zip files.
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98 if(exists("zipfile") && (zipfile!="")) {
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99 if(!file.exists(zipfile)){
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100 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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101 print(error_message)
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102 stop(error_message)
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103 }
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104
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105 #list all file in the zip file
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106 #zip_files=unzip(zipfile,list=T)[,"Name"]
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107
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108 # Because IPO only want raw data in its working directory
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109 dir.create("ipoworkingdir")
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110 setwd("ipoworkingdir")
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111 file.symlink(zipfile, ".")
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112
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113 #unzip
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114 suppressWarnings(unzip(zipfile, unzip="unzip"))
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115
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116 #get the directory name
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117 filesInZip=unzip(zipfile, list=T);
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118 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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119 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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120 directory = "."
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121 if (length(directories) == 1) directory = directories
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122
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123 cat("files_root_directory\t",directory,"\n")
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124
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125 file.remove(basename(zipfile))
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126
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127
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128 }
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129
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130 #addition of the directory to the list of arguments in the first position
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131 checkXmlStructure(directory)
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132 checkFilesCompatibilityWithXcms(directory)
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133
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134 cat("\n\n")
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135
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136
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137
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138
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139
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140
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141 # ----- MAIN PROCESSING INFO -----
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142 cat("\tMAIN PROCESSING INFO\n")
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143
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144
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145 ipo4retgroup(xset, directory, parametersOutput, listArguments, samplebyclass)
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146
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147
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148
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149 cat("\n\n")
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150
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151
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152 # ----- EXPORT -----
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153
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154 cat("\tEXPORTING INFO\n")
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155
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156 #save.image(file="ipo-retcor.RData")
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157
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158 cat("\n\n")
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159
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160
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161 cat("\tDONE\n")