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planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
author workflow4metabolomics
date Mon, 11 Sep 2023 22:40:34 +0000
parents abf1775ac14d
children
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1 # lib.r
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2
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3 # @author G. Le Corguille
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4 # solve an issue with batch if arguments are logical TRUE/FALSE
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5 parseCommandArgs <- function(...) {
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6 args <- batch::parseCommandArgs(...)
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7 for (key in names(args)) {
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8 if (args[key] %in% c("TRUE", "FALSE")) {
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9 args[key] <- as.logical(args[key])
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10 }
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11 }
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12 return(args)
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13 }
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15 # @author G. Le Corguille
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16 # This function will
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
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22 sessioninfo <- sessionInfo()
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23 cat(sessioninfo$R.version$version.string, "\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) {
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
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27 }
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28 cat("\n")
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29 cat("Other loaded packages:\n")
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30 for (pkg in names(sessioninfo$loadedOnly)) {
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
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32 }
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33 cat("\n")
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34 }
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36 # This function retrieve a xset like object
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37 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
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38 getxcmsSetObject <- function(xobject) {
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39 # XCMS 1.x
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40 if (class(xobject) == "xcmsSet") {
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41 return(xobject)
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42 }
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43 # XCMS 3.x
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44 if (class(xobject) == "XCMSnExp") {
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45 # Get the legacy xcmsSet object
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46 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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47 if (is.null(xset@phenoData$sample_group)) {
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48 sampclass(xset) <- "."
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49 } else {
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50 sampclass(xset) <- xset@phenoData$sample_group
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51 }
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52 if (!is.null(xset@phenoData$sample_name)) {
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53 rownames(xset@phenoData) <- xset@phenoData$sample_name
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54 }
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55 return(xset)
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56 }
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57 }
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58
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59 # @author G. Le Corguille
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60 # The function create a pdf from the different png generated by diffreport
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61 diffreport_png2pdf <- function(filebase) {
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62 dir.create("pdf")
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64 pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf")
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65 pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf")
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67 system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput))
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68 system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput))
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69 }
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70
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71 # @author G. Le Corguille
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72 # The function create a zip archive from the different png generated by diffreport
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73 diffreport_png2zip <- function() {
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74 zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip"))
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75 zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip"))
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76 }
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77
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78 # The function create a zip archive from the different tabular generated by diffreport
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79 diffreport_tabular2zip <- function() {
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80 zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip"))
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81 }
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82
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83 # @author G. Le Corguille
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84 # This function convert if it is required the Retention Time in minutes
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85 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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86 if (convertRTMinute) {
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87 # converting the retention times (seconds) into minutes
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88 print("converting the retention times into minutes in the variableMetadata")
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89 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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90 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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91 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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92 }
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93 return(variableMetadata)
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94 }
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95
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96 # @author G. Le Corguille
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97 # This function format ions identifiers
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98 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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99 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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100 idsDeco <- sapply(splitDeco, function(x) {
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101 deco <- unlist(x)[2]
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102 if (is.na(deco)) {
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103 return("")
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104 } else {
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105 return(paste0("_", deco))
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106 }
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107 })
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108 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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109 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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110 return(variableMetadata)
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111 }
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112
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113 # The function annotateDiffreport without the corr function which bugs
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114 annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") {
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115 # Resolve the bug with x11, with the function png
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116 options(bitmapType = "cairo")
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117
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118 # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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119 res <- try(is.null(xset@filled))
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120
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121 # ------ annot -------
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122 args$calcCiS <- as.logical(args$calcCiS)
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123 args$calcIso <- as.logical(args$calcIso)
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124 args$calcCaS <- as.logical(args$calcCaS)
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125
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126 # common parameters
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127 args4annotate <- list(
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128 object = xset,
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129 nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm,
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130 maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac,
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131 ppm = args$ppm, mzabs = args$mzabs, quick = args$quick,
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132 polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval
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133 )
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134
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135 if (args$quick == FALSE) {
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136 args4annotate <- append(
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137 args4annotate,
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138 list(
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139 graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval,
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140 calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS
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141 )
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142 )
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143 # no ruleset
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144 if (!is.null(args$multiplier)) {
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145 args4annotate <- append(
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146 args4annotate,
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147 list(multiplier = args$multiplier)
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148 )
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149 } else { # ruleset
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150 rulset <- read.table(args$rules, h = TRUE, sep = ";")
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151 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = "\t")
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152 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = TRUE, sep = ",")
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153 if (ncol(rulset) < 4) {
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154 error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
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155 print(error_message)
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156 stop(error_message)
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157 }
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158
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159 args4annotate <- append(
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160 args4annotate,
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161 list(rules = rulset)
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162 )
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163 }
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164 }
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165
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166
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167 # launch annotate
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168 xa <- do.call("annotate", args4annotate)
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169 peakList <- getPeaklist(xa, intval = args$intval)
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170 peakList <- cbind(groupnames(xa@xcmsSet), peakList)
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171 colnames(peakList)[1] <- c("name")
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172
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173 # --- Multi condition : diffreport ---
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174 diffrepOri <- NULL
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175 if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) >= 2) {
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176 # Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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177 res <- try(is.null(xset@filled))
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178 classes <- levels(sampclass(xset))
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179 for (i in seq_len(length(classes) - 1)) {
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180 for (n in seq_len(length(classes))) {
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181 if (i + n <= length(classes)) {
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182 filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-")
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183
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184 diffrep <- diffreport(
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185 object = xset, class1 = classes[i], class2 = classes[i + n],
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186 filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth,
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187 sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0
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188 )
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189
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190 diffrepOri <- diffrep
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191
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192 # renamming of the column rtmed to rt to fit with camera peaklist function output
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193 colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt"
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194 colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz"
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195
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196 # combines results and reorder columns
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197 diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
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198 diffrep <- cbind(diffrep[, !(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))], diffrep[, (colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
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199
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200 diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute)
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201 diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
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202
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203 if (args$sortpval) {
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204 diffrep <- diffrep[order(diffrep$pvalue), ]
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205 }
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206
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207 dir.create("tabular", showWarnings = FALSE)
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208 write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = ""))
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209
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210 if (args$eicmax != 0) {
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211 if (args$png2 == "pdf") {
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212 diffreport_png2pdf(filebase)
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213 }
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214 if (args$png2 == "zip") {
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215 diffreport_png2zip()
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216 }
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217 }
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218 }
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219 }
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220 }
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221 if (args$tabular2 == "zip") {
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222 diffreport_tabular2zip()
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223 }
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224 }
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225
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226 # --- variableMetadata ---
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227 variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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228 variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute)
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229 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
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230 # if we have 2 conditions, we keep stat of diffrep
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231 if (!is.null(args$runDiffreport) && nlevels(sampclass(xset)) == 2) {
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232 variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = FALSE)
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233 if (exists("args[[\"sortpval\"]]")) {
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234 variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ]
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235 }
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236 }
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237
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238 variableMetadataOri <- variableMetadata
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239 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
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240
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241 return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri))
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242 }
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243
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244
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245 combinexsAnnos_function <- function(
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246 xaP, xaN, diffrepP = NULL, diffrepN = NULL,
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247 pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = FALSE, numDigitsMZ = 0,
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248 numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") {
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249 # Load the two Rdata to extract the xset objects from positive and negative mode
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250 cat("\tObject xset from positive mode\n")
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251 print(xaP)
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252 cat("\n")
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253
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254 cat("\tObject xset from negative mode\n")
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255 print(xaN)
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256 cat("\n")
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257
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258 cat("\n")
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259 cat("\tCombining...\n")
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260 # Convert the string to numeric for creating matrix
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261 row <- as.numeric(strsplit(ruleset, ",")[[1]][1])
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262 column <- as.numeric(strsplit(ruleset, ",")[[1]][2])
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263 ruleset <- cbind(row, column)
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264 # Test if the file comes from an older version tool
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265 if ((!is.null(xaP)) && (!is.null(xaN))) {
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266 # Launch the combinexsannos function from CAMERA
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267 cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset)
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268 } else {
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269 stop("You must relauch the CAMERA.annotate step with the lastest version.")
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270 }
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271
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272 if (pos) {
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273 xa <- xaP
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274 mode <- "neg. Mode"
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275 } else {
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276 xa <- xaN
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277 mode <- "pos. Mode"
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278 }
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279
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280 peakList <- getPeaklist(xa)
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281 peakList <- cbind(groupnames(xa@xcmsSet), peakList)
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282 colnames(peakList)[1] <- c("name")
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283 variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)])
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284 variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
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285
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286 # Test if there are more than two classes (conditions)
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287 if (nlevels(sampclass(xaP@xcmsSet)) == 2 && (!is.null(diffrepN)) && (!is.null(diffrepP))) {
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288 diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]
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289 colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "")
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290 diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]
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291 colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "")
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292
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293 variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name")
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294 variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name")
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295 }
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296
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297 rownames(variableMetadata) <- NULL
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298 # TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt");
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299
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300 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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301 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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302
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303 # If the user want to keep only the metabolites which match a difference
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304 if (keep_meta) {
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305 variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ]
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306 }
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307
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308 # Write the output into a tsv file
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309 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
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310 return(variableMetadata)
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311 }
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312
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313 # This function get the raw file path from the arguments
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314 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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315 if (!is.null(args$zipfile)) zipfile <- args$zipfile
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316 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
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317 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
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318
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319 if (!is.null(args$singlefile_galaxyPath)) {
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320 singlefile_galaxyPaths <- args$singlefile_galaxyPath
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321 singlefile_sampleNames <- args$singlefile_sampleName
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322 }
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323 if (!is.null(args$singlefile_galaxyPathPositive)) {
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324 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive
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325 singlefile_sampleNames <- args$singlefile_sampleNamePositive
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326 }
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327 if (!is.null(args$singlefile_galaxyPathNegative)) {
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328 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative
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329 singlefile_sampleNames <- args$singlefile_sampleNameNegative
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330 }
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331 if (exists("singlefile_galaxyPaths")) {
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332 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ","))
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333 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ","))
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334
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335 singlefile <- NULL
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336 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
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337 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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338 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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339 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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340 }
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341 }
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342 for (argument in c(
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343 "zipfile", "zipfilePositive", "zipfileNegative",
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344 "singlefile_galaxyPath", "singlefile_sampleName",
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345 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
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346 "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative"
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347 )) {
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348 args[[argument]] <- NULL
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349 }
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350 return(list(zipfile = zipfile, singlefile = singlefile, args = args))
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351 }
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352
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353
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354 # This function retrieve the raw file in the working directory
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355 # - if zipfile: unzip the file with its directory tree
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356 # - if singlefiles: set symlink with the good filename
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357 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) {
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358 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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359 for (singlefile_sampleName in names(singlefile)) {
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360 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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361 if (!file.exists(singlefile_galaxyPath)) {
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362 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
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363 print(error_message)
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364 stop(error_message)
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365 }
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366
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367 file.symlink(singlefile_galaxyPath, singlefile_sampleName)
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368 }
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369 directory <- "."
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370 }
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371 if (!is.null(zipfile) && (zipfile != "")) {
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372 if (!file.exists(zipfile)) {
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373 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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374 print(error_message)
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375 stop(error_message)
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376 }
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377
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378 # unzip
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379 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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380
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381 # get the directory name
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382 filesInZip <- unzip(zipfile, list = TRUE)
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383 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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384 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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385 directory <- "."
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386 if (length(directories) == 1) directory <- directories
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387
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388 cat("files_root_directory\t", directory, "\n")
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389 }
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390 return(directory)
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391 }