Mercurial > repos > eschen42 > xcms_refine

annotate xcms_refine.r @ 0:ae9ef9219aae draft default tip

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
author eschen42
date Fri, 12 Feb 2021 18:05:29 +0000
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1 #!/usr/bin/env Rscript
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3 # ----- LOG FILE -----
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4 log_file=file("log.txt", open = "wt")
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5 sink(log_file)
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6 sink(log_file, type = "output")
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 #Import the different functions
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13 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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14 source_local("lib.r")
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16 pkgs <- c("xcms","batch","RColorBrewer")
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17 loadAndDisplayPackages(pkgs)
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18 cat("\n\n");
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20 # ----- EXPLORE NAMESPACE -----
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21 # cat("\tXCMS NAMESPACE INFO\n")
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22 # ls(asNamespace("xcms"))
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24 # ----- ARGUMENTS -----
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25 cat("\tARGUMENTS INFO\n")
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26 args <- 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(args), col.names=F, quote=F, sep='\t')
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29 cat("\n\n")
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31 # ----- PROCESSING INFILE -----
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32 cat("\tARGUMENTS PROCESSING INFO\n")
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34 #saving the specific parameters
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35 args_method <- args$method
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36 args_image <- args$image
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37 args_msLevel <- args$msLevel
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38 #args[c('method','image','msLevel')] <- NULL
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39 param_args <- list()
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41 if ( args_method == "CleanPeaks" ) {
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42 param_args$maxPeakwidth <- as.numeric(args$maxPeakwidth)
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43 if (is.na(as.numeric(param_args$maxPeakwidth))) stop("\n\nERROR: The maxPeakwidth argument cannot be coerced to a numeric value.")
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44 } else if ( args_method == "FilterIntensity" ) {
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45 param_args$threshold <- as.numeric(args$threshold)
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46 if (is.na(as.numeric(param_args$threshold))) stop("\n\nERROR: The threshold argument cannot be coerced to a numeric value.")
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47 param_args$nValues <- as.numeric(args$nValues)
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48 if (is.na(as.numeric(param_args$nValues))) stop("\n\nERROR: The nValues argument cannot be coerced to a numeric value.")
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49 if (as.integer(param_args$nValues) != param_args$nValues) stop("\n\nERROR: The nValues argument is not an integer value.")
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50 param_args$value <- args$value
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51 } else if ( args_method == "MergeNeighboringPeaks" ) {
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52 if (is.na(as.numeric(args$expandRt))) stop("\n\nERROR: The expandRt argument cannot be coerced to a numeric value.")
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53 if (is.na(as.numeric(args$expandMz))) stop("\n\nERROR: The expandMz argument cannot be coerced to a numeric value.")
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54 if (is.na(as.numeric(args$ppm))) stop("\n\nERROR: The ppm argument cannot be coerced to a numeric value.")
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55 if (is.na(as.numeric(args$minProp))) stop("\n\nERROR: The minProp argument cannot be coerced to a numeric value.")
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56 param_args$expandRt <- args$expandRt
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57 param_args$expandMz <- args$expandMz
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58 param_args$ppm <- args$ppm
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59 param_args$minProp <- args$minProp
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60 }
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62 cat("\n\n")
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65 # ----- ARGUMENTS PROCESSING -----
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66 cat("\tINFILE PROCESSING INFO\n")
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67
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68 #image is an .RData file necessary to use xset variable given by previous tools
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69 load(args_image)
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70 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
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72 # Handle infiles
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73 if (!exists("singlefile")) singlefile <- NULL
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74 if (!exists("zipfile")) zipfile <- NULL
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75 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
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76 zipfile <- rawFilePath$zipfile
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77 singlefile <- rawFilePath$singlefile
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79 cat("\n\n")
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82 # ----- MAIN PROCESSING INFO -----
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83 cat("\tMAIN PROCESSING INFO\n")
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84
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85
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86 cat("\t\tPREPARE PARAMETERS\n\n")
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87
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88 if ( args_method == "CleanPeaks" ) {
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89 refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
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90 } else if ( args_method == "FilterIntensity" ) {
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91 refineChromPeaksParam <- FilterIntensityParam(
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92 threshold = param_args$threshold,
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93 nValues = param_args$nValues,
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94 value = param_args$value
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95 )
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96 } else if ( args_method == "MergeNeighboringPeaks" ) {
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97 refineChromPeaksParam <- MergeNeighboringPeaksParam(
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98 expandRt = param_args$expandRt,
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99 expandMz = param_args$expandMz,
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100 ppm = param_args$ppm,
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101 minProp = param_args$minProp
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102 )
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103 }
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104
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105 cat(str(refineChromPeaksParam))
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106
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107 cat("\n\n\t\tCOMPUTE\n")
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108
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109 # cat("\t\t\tACE DEBUG show the xdata\n")
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110 # cat(str(xdata))
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111 # cat("\n\t\t\tACE DEBUG (end show the xdata)\n")
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112
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113 # cat("\t\t\tACE DEBUG show updateObject(xdata)\n")
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114 xdata <- updateObject(xdata)
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115 # cat(str(xdata))
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116 # cat("\n\t\t\tACE DEBUG (end show updateObject(xdata))\n")
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117 #
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118 # cat("\t\t\tACE DEBUG show the param_args\n")
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119 # cat(str(param_args))
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120 # cat("\n\t\t\tACE DEBUG (end show the param_args)\n")
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121 #
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122 # cat("\t\t\tACE DEBUG show the refineChromPeaksParam\n")
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123 # cat(str(refineChromPeaksParam))
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124 # cat("\n\t\t\tACE DEBUG (end show the refineChromPeaksParam)\n")
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125 #
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126 # cat("\t\t\tACE DEBUG show the slotNames\n")
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127 # cat(str(slotNames(refineChromPeaksParam)))
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128 # cat("\n\t\t\tACE DEBUG (end show the slotNames)\n")
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129
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130 # # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or args_method ...
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131 # param_args <- param_args[names(param_args) %in% slotNames(do.call(paste0(args_method,"Param"), param_args))]
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132 #
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133 # refineChromPeaksParam <- do.call(paste0(args_method,"Param"), param_args)
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134 # print(refineChromPeaksParam)
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135
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136 # cat("\t\t\tACE DEBUG invoke refineChromPeaks\n")
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137 xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
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138 # cat("\t\t\tACE DEBUG returned from refineChromPeaks\n")
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139 #
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140 #
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141 # cat("\t\tDRAW GRAPHICS\n")
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142 # getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
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143 #
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144 # if (exists("intval")) {
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145 # getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
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146 # }
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147 #
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148 cat("\n\n")
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149
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150 # ----- EXPORT -----
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151
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152 cat("\tXCMSnExp OBJECT INFO\n")
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153 print(xdata)
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154 cat("\n\n")
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155
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156 cat("\txcmsSet OBJECT INFO\n")
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157 # Get the legacy xcmsSet object
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158 xset <- getxcmsSetObject(xdata)
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159 print(xset)
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160 cat("\n\n")
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161
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162 #saving R data in .Rdata file to save the variables used in the present tool
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163 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
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164 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
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165
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166 cat("\n\n")
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167
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168
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169 cat("\tDONE\n")