annotate lib.r @ 27:ec9aebabc1d2 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:58:27 +0000
parents bb9ee352fce0
children
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1 #@authors ABiMS TEAM, Y. Guitton
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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4 #@author G. Le Corguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
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6 parseCommandArgs <- function(...) {
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7 args <- batch::parseCommandArgs(...)
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8 for (key in names(args)) {
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9 if (args[key] %in% c("TRUE", "FALSE"))
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10 args[key] <- as.logical(args[key])
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11 }
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12 return(args)
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13 }
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14
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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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21
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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 #@author G. Le Corguille
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37 # This function merge several chromBPI or chromTIC into one.
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38 mergeChrom <- function(chrom_merged, chrom) {
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39 if (is.null(chrom_merged)) return(NULL)
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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41 return(chrom_merged)
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42 }
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44 #@author G. Le Corguille
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45 # This function merge several xdata into one.
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46 mergeXData <- function(args) {
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47 chromTIC <- NULL
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48 chromBPI <- NULL
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49 chromTIC_adjusted <- NULL
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50 chromBPI_adjusted <- NULL
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51 md5sumList <- NULL
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52 for (image in args$images) {
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53
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54 load(image)
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55 # Handle infiles
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56 if (!exists("singlefile")) singlefile <- NULL
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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60 singlefile <- rawFilePath$singlefile
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61
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62 if (exists("raw_data")) xdata <- raw_data
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
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68 xdata_merged <- xdata
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69 singlefile_merged <- singlefile
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70 md5sumList_merged <- md5sumList
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71 sampleNamesList_merged <- sampleNamesList
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72 chromTIC_merged <- chromTIC
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73 chromBPI_merged <- chromBPI
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
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76 } else {
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
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79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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80
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81 singlefile_merged <- c(singlefile_merged, singlefile)
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
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91 rm(image)
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92 xdata <- xdata_merged
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93 rm(xdata_merged)
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94 singlefile <- singlefile_merged
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95 rm(singlefile_merged)
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96 md5sumList <- md5sumList_merged
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97 rm(md5sumList_merged)
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98 sampleNamesList <- sampleNamesList_merged
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99 rm(sampleNamesList_merged)
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100
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101 if (!is.null(args$sampleMetadata)) {
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102 cat("\tXSET PHENODATA SETTING...\n")
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103 sampleMetadataFile <- args$sampleMetadata
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104 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
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105 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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106
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107 if (any(is.na(pData(xdata)$sample_group))) {
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108 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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109 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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110 print(error_message)
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111 stop(error_message)
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112 }
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113 }
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114
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115 if (!is.null(chromTIC_merged)) {
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116 chromTIC <- chromTIC_merged
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117 chromTIC@phenoData <- xdata@phenoData
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118 }
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119 if (!is.null(chromBPI_merged)) {
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120 chromBPI <- chromBPI_merged
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121 chromBPI@phenoData <- xdata@phenoData
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122 }
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123 if (!is.null(chromTIC_adjusted_merged)) {
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124 chromTIC_adjusted <- chromTIC_adjusted_merged
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125 chromTIC_adjusted@phenoData <- xdata@phenoData
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126 }
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127 if (!is.null(chromBPI_adjusted_merged)) {
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128 chromBPI_adjusted <- chromBPI_adjusted_merged
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129 chromBPI_adjusted@phenoData <- xdata@phenoData
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130 }
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131
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132 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
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133 }
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134
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135 #@author G. Le Corguille
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136 # This function convert if it is required the Retention Time in minutes
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137 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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138 if (convertRTMinute) {
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139 #converting the retention times (seconds) into minutes
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140 print("converting the retention times into minutes in the variableMetadata")
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141 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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142 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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143 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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144 }
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145 return(variableMetadata)
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146 }
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147
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148 #@author G. Le Corguille
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149 # This function format ions identifiers
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150 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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151 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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152 idsDeco <- sapply(splitDeco,
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153 function(x) {
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154 deco <- unlist(x)[2]
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155 if (is.na(deco)) return("") else return(paste0("_", deco))
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156 }
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157 )
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158 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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159 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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160 return(variableMetadata)
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161 }
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162
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163 #@author G. Le Corguille
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164 # This function convert the remain NA to 0 in the dataMatrix
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165 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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166 if (naTOzero) {
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167 dataMatrix[is.na(dataMatrix)] <- 0
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168 }
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169 return(dataMatrix)
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170 }
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171
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172 #@author G. Le Corguille
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173 # Draw the plotChromPeakDensity 3 per page in a pdf file
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174 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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175 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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176
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177 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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178
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179 if (length(unique(xdata$sample_group)) < 10) {
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180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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181 } else {
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182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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183 }
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184 names(group_colors) <- unique(xdata$sample_group)
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185 col_per_samp <- as.character(xdata$sample_group)
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186 for (i in seq_len(length(group_colors))) {
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187 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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188 }
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189
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190 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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191 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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192 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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193 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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194 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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195 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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196 }
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197
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198 dev.off()
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199 }
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200
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201 #@author G. Le Corguille
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202 # Draw the plotChromPeakDensity 3 per page in a pdf file
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203 getPlotAdjustedRtime <- function(xdata) {
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204
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205 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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206
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207 # Color by group
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208 if (length(unique(xdata$sample_group)) < 10) {
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209 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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210 } else {
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211 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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212 }
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213 if (length(group_colors) > 1) {
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214 names(group_colors) <- unique(xdata$sample_group)
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215 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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216 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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217 }
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218
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219 # Color by sample
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220 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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221 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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222
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223 dev.off()
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224 }
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225
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226 #@author G. Le Corguille
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227 # value: intensity values to be used into, maxo or intb
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228 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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229 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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230 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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231 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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232 variableMetadata <- featureDefinitions(xdata)
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233 colnames(variableMetadata)[1] <- "mz"
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234 colnames(variableMetadata)[4] <- "rt"
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235 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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236
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237 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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238 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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239 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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240
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241 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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242 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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243
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244 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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245 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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246
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247 }
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248
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249 #@author G. Le Corguille
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250 # It allow different of field separators
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251 getDataFrameFromFile <- function(filename, header = TRUE) {
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252 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
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253 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
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254 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
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255 if (ncol(myDataFrame) < 2) {
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256 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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257 print(error_message)
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258 stop(error_message)
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259 }
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260 return(myDataFrame)
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261 }
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262
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263 #@author G. Le Corguille
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264 # Draw the BPI and TIC graphics
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265 # colored by sample names or class names
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26d77e9ceb49 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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266 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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267
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268 if (aggregationFun == "sum")
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269 type <- "Total Ion Chromatograms"
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270 else
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271 type <- "Base Peak Intensity Chromatograms"
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272
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273 adjusted <- "Raw"
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274 if (hasAdjustedRtime(xdata))
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275 adjusted <- "Adjusted"
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276
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277 main <- paste(type, ":", adjusted, "data")
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278
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279 pdf(pdfname, width = 16, height = 10)
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280
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281 # Color by group
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282 if (length(unique(xdata$sample_group)) < 10) {
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283 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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284 } else {
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285 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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286 }
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287 if (length(group_colors) > 1) {
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288 names(group_colors) <- unique(xdata$sample_group)
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289 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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290 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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291 }
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292
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293 # Color by sample
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294 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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295 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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296
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297 dev.off()
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298 }
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299
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300
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301 # Get the polarities from all the samples of a condition
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302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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26d77e9ceb49 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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305 cat("Creating the sampleMetadata file...\n")
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306
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307 #Create the sampleMetada dataframe
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308 sampleMetadata <- xdata@phenoData@data
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309 rownames(sampleMetadata) <- NULL
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310 colnames(sampleMetadata) <- c("sample_name", "class")
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311
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312 sampleNamesOrigin <- sampleMetadata$sample_name
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313 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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314
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315 if (any(duplicated(sampleNamesMakeNames))) {
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316 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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317 for (sampleName in sampleNamesOrigin) {
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318 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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319 }
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320 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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321 }
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322
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323 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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324 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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325 for (sampleName in sampleNamesOrigin) {
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326 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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327 }
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328 }
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329
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330 sampleMetadata$sample_name <- sampleNamesMakeNames
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331
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332
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333 #For each sample file, the following actions are done
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334 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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335 #Check if the file is in the CDF format
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336 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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337
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338 # If the column isn't exist, with add one filled with NA
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339 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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340
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341 #Extract the polarity (a list of polarities)
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342 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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343 #Verify if all the scans have the same polarity
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344 uniq_list <- unique(polarity)
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345 if (length(uniq_list) > 1) {
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346 polarity <- "mixed"
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347 } else {
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348 polarity <- as.character(uniq_list)
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349 }
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350
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351 #Set the polarity attribute
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352 sampleMetadata$polarity[fileIdx] <- polarity
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353 }
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354
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355 }
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356
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357 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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358
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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359 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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360
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361 }
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362
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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363
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lecorguille
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364 # This function will compute MD5 checksum to check the data integrity
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2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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26d77e9ceb49 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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366 getMd5sum <- function(files) {
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367 cat("Compute md5 checksum...\n")
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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368 library(tools)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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369 return(as.matrix(md5sum(files)))
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370 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
371
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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372 # This function retrieve the raw file in the working directory
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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373 # - if zipfile: unzip the file with its directory tree
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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374 # - if singlefiles: set symlink with the good filename
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375 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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26d77e9ceb49 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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376 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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377
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378 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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379
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380 # single - if the file are passed in the command arguments -> refresh singlefile
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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384
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385 singlefile <- NULL
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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389 # In case, an url is used to import data within Galaxy
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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390 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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392 }
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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393 }
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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395 if (!is.null(args[[paste0("zipfile", prefix)]]))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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396 zipfile <- args[[paste0("zipfile", prefix)]]
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397
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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398 # single
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399 if (!is.null(singlefile) && (length("singlefile") > 0)) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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400 files <- vector()
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
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401 for (singlefile_sampleName in names(singlefile)) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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403 if (!file.exists(singlefile_galaxyPath)) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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404 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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405 print(error_message)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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406 stop(error_message)
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407 }
4
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408
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bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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409 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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410 file.copy(singlefile_galaxyPath, singlefile_sampleName)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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411 files <- c(files, singlefile_sampleName)
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412 }
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413 }
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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414 # zipfile
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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415 if (!is.null(zipfile) && (zipfile != "")) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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416 if (!file.exists(zipfile)) {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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418 print(error_message)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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419 stop(error_message)
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420 }
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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422
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423 #get the directory name
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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424 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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425 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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426 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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427 directory <- "."
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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428 if (length(directories) == 1) directory <- directories
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diff changeset
429
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430 cat("files_root_directory\t", directory, "\n")
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431
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432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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434 info <- file.info(directory)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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436 files <- c(directory[!info$isdir], listed)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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437 exists <- file.exists(files)
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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438 files <- files[exists]
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999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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439
26
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440 }
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
4
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lecorguille
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diff changeset
442 }
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lecorguille
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diff changeset
443
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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444
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
445 # This function retrieve a xset like object
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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447 getxcmsSetObject <- function(xobject) {
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448 # XCMS 1.x
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449 if (class(xobject) == "xcmsSet")
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450 return(xobject)
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451 # XCMS 3.x
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452 if (class(xobject) == "XCMSnExp") {
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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453 # Get the legacy xcmsSet object
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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455 if (!is.null(xset@phenoData$sample_group))
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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456 sampclass(xset) <- xset@phenoData$sample_group
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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457 else
bb9ee352fce0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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458 sampclass(xset) <- "."
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459 return(xset)
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460 }
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91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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461 }