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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2
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3 ## 08122016_ReadFids_wrapper.R
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4 ## Manon Martin
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5 ## manon.martin@uclouvain.be
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6
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7 ##======================================================
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8 ##======================================================
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9 # Preamble
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10 ##======================================================
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11 ##======================================================
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12
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13 runExampleL <- FALSE
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14
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15
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16 ##------------------------------
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17 ## Options
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18 ##------------------------------
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19 strAsFacL <- options()$stringsAsFactors
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20 options(stringsAsFactors = FALSE)
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21 options(warn=1)
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22
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23 ##------------------------------
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24 ## Libraries laoding
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25 ##------------------------------
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26 library(batch)
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27 library(ggplot2)
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28 library(gridExtra)
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29 library(reshape2)
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30
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31
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32 # R script call
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33 source_local <- function(fname)
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34 {
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35 argv <- commandArgs(trailingOnly = FALSE)
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36 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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37 source(paste(base_dir, fname, sep="/"))
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38 }
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39 #Import the different functions
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40 source_local("ReadFids_script.R")
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41 source_local("DrawFunctions.R")
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42 ##------------------------------
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43 ## Errors ?????????????????????
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44 ##------------------------------
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45
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46
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47 ##------------------------------
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48 ## Constants
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49 ##------------------------------
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50 topEnvC <- environment()
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51 flagC <- "\n"
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52
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53
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54 ##------------------------------
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55 ## Script
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56 ##------------------------------
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57 if(!runExampleL)
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58 argLs <- parseCommandArgs(evaluate=FALSE)
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59
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60 sink(argLs$logOut)
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61
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62 ##======================================================
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63 ##======================================================
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64 ## Parameters Loading
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65 ##======================================================
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66 ##======================================================
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67
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68 ## Inputs
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69 # Path
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70 ## Bruker FIDs
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71 fileType="Bruker"
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72 zipfile= argLs[["fidzipfile"]]
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73 directory=unzip(zipfile, list=F)
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74 path=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
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75
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76
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77 # other inputs from ReadFids
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78 l = argLs[["title_line"]]
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79 subdirs <- argLs[["subdirectories"]]
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80 dirs.names <- argLs[["dirs_names"]]
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81
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82
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83 # Outputs
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84 # dataMatrix <- argLs[["dataMatrix"]]
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85 # sampleMetadata <- argLs[["sampleMetadata"]]
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86 logOut <- argLs[["logOut"]]
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87 nomGraphe <- argLs[["graphOut"]]
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88
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89
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90
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91 ## Checking arguments
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92 ##-------------------
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93 error.stock <- "\n"
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94
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95 if(length(error.stock) > 1)
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96 stop(error.stock)
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97
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98
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99
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100 ##======================================================
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101 ##======================================================
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102 ## Computation
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103 ##======================================================
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104 ##======================================================
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105 sink(logOut,append=TRUE)
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106
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107 if(length(warnings())>0){ # or !is.null(warnings())
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108 print("something happened")
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109 }
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110
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111 ## Starting
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112 cat("\nStart of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), "\n\n", sep = "")
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113
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114 outputs <- ReadFids(path = path, l=l, subdirs = subdirs, dirs.names = dirs.names)
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115
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116 data_matrix <- outputs[["Fid_data"]] # Data matrix
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117 data_sample <- outputs[["Fid_info"]] # Sample metadata
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118
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119
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120
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121 pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
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122 title = "Raw FID data"
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123 DrawSignal(data_matrix, subtype = "stacked",
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124 ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
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125 xlab = "Frequency", num.stacked = 4,
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126 main = title, createWindow=FALSE)
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127 invisible(dev.off())
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128
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129 ##======================================================
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130 ##======================================================
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131 ## Saving
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132 ##======================================================
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133 ##======================================================
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134
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135 # Data matrix
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136 write.table(data_matrix,file=argLs$dataMatrix, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
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137
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138 # Sample metadata
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139 write.table(data_sample,file=argLs$sampleMetadata, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
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140
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141 # log file
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142 # write.table(t(data.frame(argLs)), file = argLs$logOut, col.names = FALSE, quote=FALSE)
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143
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144 # input arguments
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145 cat("\n INPUT and OUTPUT ARGUMENTS :\n")
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146
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147 argLs
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148
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149 ## Ending
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150
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151 cat("\nEnd of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), sep = "")
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152
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153 sink()
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154
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155
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156 options(stringsAsFactors = strAsFacL)
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157
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158 rm(list = ls()) |
