Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 36:e309e6af6744 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
author lecorguille
date Fri, 31 Aug 2018 09:02:01 -0400
parents 2b0a4c7a4a48
children 35a20d7c9f33
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
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lecorguille
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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)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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13 }
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c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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15 #@author G. Le Corguille
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16 # This function will
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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lecorguille
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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")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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26 cat("Other loaded packages:\n")
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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28 }
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30 #@author G. Le Corguille
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31 # This function merge several chromBPI or chromTIC into one.
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32 mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
2b0a4c7a4a48 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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33 if (is.null(chromTIC_merged)) return(NULL)
2b0a4c7a4a48 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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34 chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
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35 chromTIC_merged@phenoData <- xdata_merged@phenoData
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36 return(chromTIC_merged)
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37 }
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lecorguille
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39 #@author G. Le Corguille
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40 # This function merge several xdata into one.
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41 mergeXData <- function(args) {
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42 chromTIC <- NULL; chromBPI <- NULL
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43 for(image in args$images) {
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44 load(image)
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45 # Handle infiles
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46 if (!exists("singlefile")) singlefile <- NULL
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47 if (!exists("zipfile")) zipfile <- NULL
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48 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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49 zipfile <- rawFilePath$zipfile
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50 singlefile <- rawFilePath$singlefile
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51 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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52 if (exists("raw_data")) xdata <- raw_data
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53 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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54 cat(sampleNamesList$sampleNamesOrigin,"\n")
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55 if (!exists("xdata_merged")) {
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56 xdata_merged <- xdata
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57 singlefile_merged <- singlefile
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58 md5sumList_merged <- md5sumList
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59 sampleNamesList_merged <- sampleNamesList
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60 chromTIC_merged <- chromTIC
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61 chromBPI_merged <- chromBPI
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62 } else {
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63 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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64 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
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65 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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66 singlefile_merged <- c(singlefile_merged,singlefile)
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67 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
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68 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
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69 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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70 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
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71 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
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72 }
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73 }
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74 rm(image)
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75 xdata <- xdata_merged; rm(xdata_merged)
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76 singlefile <- singlefile_merged; rm(singlefile_merged)
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lecorguille
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77 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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78 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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79 chromTIC <- chromTIC_merged; rm(chromTIC_merged)
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80 chromBPI <- chromBPI_merged; rm(chromBPI_merged)
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81
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82 if (!is.null(args$sampleMetadata)) {
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83 cat("\tXSET PHENODATA SETTING...\n")
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84 sampleMetadataFile <- args$sampleMetadata
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85 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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86 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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87
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88 if (any(is.na(pData(xdata)$sample_group))) {
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89 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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90 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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91 print(error_message)
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92 stop(error_message)
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93 }
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94 }
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95 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
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96 }
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97
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98 #@author G. Le Corguille
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99 # This function convert if it is required the Retention Time in minutes
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100 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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101 if (convertRTMinute){
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102 #converting the retention times (seconds) into minutes
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103 print("converting the retention times into minutes in the variableMetadata")
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104 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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105 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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106 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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107 }
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108 return (variableMetadata)
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109 }
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110
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111 #@author G. Le Corguille
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112 # This function format ions identifiers
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113 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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114 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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115 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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116 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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117 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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118 return(variableMetadata)
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119 }
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120
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121 #@author G. Le Corguille
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122 # Draw the plotChromPeakDensity 3 per page in a pdf file
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123 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
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124 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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125
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126 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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127
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128 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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129 names(group_colors) <- unique(xdata$sample_group)
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130
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131 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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132 for (i in 1:nrow(featureDefinitions(xdata))) {
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133 mzmin = featureDefinitions(xdata)[i,]$mzmin
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134 mzmax = featureDefinitions(xdata)[i,]$mzmax
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135 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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136 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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137 }
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138
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139 dev.off()
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140 }
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141
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142 #@author G. Le Corguille
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143 # Draw the plotChromPeakDensity 3 per page in a pdf file
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144 getPlotAdjustedRtime <- function(xdata) {
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145
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146 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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147
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148 # Color by group
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149 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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150 if (length(group_colors) > 1) {
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151 names(group_colors) <- unique(xdata$sample_group)
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152 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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153 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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154 }
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155
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156 # Color by sample
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157 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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158 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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159
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160 dev.off()
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161 }
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162
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163 #@author G. Le Corguille
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164 # value: intensity values to be used into, maxo or intb
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165 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
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166 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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167 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
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168 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
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169 variableMetadata <- featureDefinitions(xdata)
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170 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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171 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
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172
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173 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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174 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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175
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176 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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177 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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178
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179 }
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180
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181 #@author G. Le Corguille
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182 # It allow different of field separators
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183 getDataFrameFromFile <- function(filename, header=T) {
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184 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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185 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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186 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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187 if (ncol(myDataFrame) < 2) {
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188 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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189 print(error_message)
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190 stop(error_message)
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191 }
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192 return(myDataFrame)
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193 }
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194
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195 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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196
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197 if (aggregationFun == "sum")
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198 type="Total Ion Chromatograms"
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199 else
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200 type="Base Peak Intensity Chromatograms"
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201
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202 adjusted="Raw"
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203 if (hasAdjustedRtime(xdata))
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204 adjusted="Adjusted"
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205
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206 main <- paste(type,":",adjusted,"data")
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207
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208 pdf(pdfname, width=16, height=10)
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209
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210 # Color by group
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211 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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212 if (length(group_colors) > 1) {
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213 names(group_colors) <- unique(xdata$sample_group)
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214 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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215 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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216 }
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217
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218 # Color by sample
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219 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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220 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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221
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222 dev.off()
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223 }
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224
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225
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226 # Get the polarities from all the samples of a condition
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227 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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228 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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229 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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230 cat("Creating the sampleMetadata file...\n")
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231
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232 #Create the sampleMetada dataframe
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233 sampleMetadata <- xdata@phenoData@data
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234 rownames(sampleMetadata) <- NULL
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235 colnames(sampleMetadata) <- c("sampleMetadata", "class")
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236
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237 sampleNamesOrigin <- sampleMetadata$sampleMetadata
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238 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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239
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240 if (any(duplicated(sampleNamesMakeNames))) {
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241 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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242 for (sampleName in sampleNamesOrigin) {
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243 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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244 }
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245 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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246 }
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247
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248 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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249 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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250 for (sampleName in sampleNamesOrigin) {
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251 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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252 }
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253 }
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254
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255 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
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256
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257
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258 #For each sample file, the following actions are done
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259 for (fileIdx in 1:length(fileNames(xdata))) {
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260 #Check if the file is in the CDF format
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261 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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262
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263 # If the column isn't exist, with add one filled with NA
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264 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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265
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266 #Extract the polarity (a list of polarities)
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267 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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268 #Verify if all the scans have the same polarity
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269 uniq_list <- unique(polarity)
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270 if (length(uniq_list)>1){
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271 polarity <- "mixed"
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272 } else {
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273 polarity <- as.character(uniq_list)
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274 }
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275
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276 #Set the polarity attribute
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277 sampleMetadata$polarity[fileIdx] <- polarity
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278 }
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279
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280 }
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281
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282 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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283
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284 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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285
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286 }
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287
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288
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289 # This function check if xcms will found all the files
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290 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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291 checkFilesCompatibilityWithXcms <- function(directory) {
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292 cat("Checking files filenames compatibilities with xmcs...\n")
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293 # WHAT XCMS WILL FIND
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294 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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295 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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296 info <- file.info(directory)
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297 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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298 files <- c(directory[!info$isdir], listed)
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299 files_abs <- file.path(getwd(), files)
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300 exists <- file.exists(files_abs)
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301 files[exists] <- files_abs[exists]
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302 files[exists] <- sub("//","/",files[exists])
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303
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304 # WHAT IS ON THE FILESYSTEM
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305 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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306 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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307
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308 # COMPARISON
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309 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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310 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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311 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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312 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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313 }
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314 }
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315
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316
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317 #This function list the compatible files within the directory as xcms did
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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319 getMSFiles <- function (directory) {
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320 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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321 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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322 info <- file.info(directory)
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323 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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324 files <- c(directory[!info$isdir], listed)
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325 exists <- file.exists(files)
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326 files <- files[exists]
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327 return(files)
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328 }
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329
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330 # This function check if XML contains special caracters. It also checks integrity and completness.
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331 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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332 checkXmlStructure <- function (directory) {
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333 cat("Checking XML structure...\n")
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334
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335 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
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336 capture <- system(cmd, intern=TRUE)
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337
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338 if (length(capture)>0){
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339 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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340 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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341 write(capture, stderr())
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342 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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343 }
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344
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345 }
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346
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347
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348 # This function check if XML contain special characters
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349 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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350 deleteXmlBadCharacters<- function (directory) {
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351 cat("Checking Non ASCII characters in the XML...\n")
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352
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353 processed <- F
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354 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
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355 for (i in l){
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356 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
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357 capture <- suppressWarnings(system(cmd, intern=TRUE))
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358 if (length(capture)>0){
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359 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
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360 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
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361 c <- system(cmd, intern=TRUE)
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362 capture <- ""
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363 processed <- T
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364 }
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365 }
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366 if (processed) cat("\n\n")
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367 return(processed)
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368 }
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369
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370
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371 # This function will compute MD5 checksum to check the data integrity
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372 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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373 getMd5sum <- function (directory) {
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374 cat("Compute md5 checksum...\n")
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375 # WHAT XCMS WILL FIND
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376 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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377 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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378 info <- file.info(directory)
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379 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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380 files <- c(directory[!info$isdir], listed)
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381 exists <- file.exists(files)
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382 files <- files[exists]
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383
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384 library(tools)
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385
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386 #cat("\n\n")
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387
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388 return(as.matrix(md5sum(files)))
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389 }
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390
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391
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392 # This function get the raw file path from the arguments
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393 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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394 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
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395 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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396
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397 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
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398
36
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399 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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400 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
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401 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
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402 }
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403 if (exists("singlefile_galaxyPaths")){
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404 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
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405 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
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406
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407 singlefile <- NULL
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408 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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409 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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410 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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411 # In case, an url is used to import data within Galaxy
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412 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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413 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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414 }
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415 }
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416 return(list(zipfile=zipfile, singlefile=singlefile))
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417 }
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418
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419 # This function retrieve the raw file in the working directory
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420 # - if zipfile: unzip the file with its directory tree
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421 # - if singlefiles: set symlink with the good filename
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422 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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423 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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424 if(!is.null(singlefile) && (length("singlefile")>0)) {
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425 for (singlefile_sampleName in names(singlefile)) {
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426 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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427 if(!file.exists(singlefile_galaxyPath)){
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428 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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429 print(error_message); stop(error_message)
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430 }
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431
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432 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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433 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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434
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435 }
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436 directory <- "."
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437
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438 }
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439 if(!is.null(zipfile) && (zipfile != "")) {
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440 if(!file.exists(zipfile)){
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441 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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442 print(error_message)
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443 stop(error_message)
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444 }
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445
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446 #list all file in the zip file
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447 #zip_files <- unzip(zipfile,list=T)[,"Name"]
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448
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449 #unzip
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450 suppressWarnings(unzip(zipfile, unzip="unzip"))
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451
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452 #get the directory name
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453 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
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454 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
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455 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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456 directory <- "."
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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457 if (length(directories) == 1) directory <- directories
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458
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459 cat("files_root_directory\t",directory,"\n")
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460
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461 }
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462 return (directory)
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463 }
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464
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465
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466 # This function retrieve a xset like object
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467 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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468 getxcmsSetObject <- function(xobject) {
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469 # XCMS 1.x
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470 if (class(xobject) == "xcmsSet")
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471 return (xobject)
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472 # XCMS 3.x
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473 if (class(xobject) == "XCMSnExp") {
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474 # Get the legacy xcmsSet object
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475 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
36
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476 if (!is.null(xset@phenoData$sample_group))
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477 sampclass(xset) <- xset@phenoData$sample_group
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478 else
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479 sampclass(xset) <- "."
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480 return (xset)
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481 }
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482 }
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483
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484
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485 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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486 # https://github.com/sneumann/xcms/issues/250
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487 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
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488 mzfmt <- paste("%.", mzdec, "f", sep = "")
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489 rtfmt <- paste("%.", rtdec, "f", sep = "")
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490
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491 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
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492 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
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493
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494 if (any(dup <- duplicated(gnames)))
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495 for (dupname in unique(gnames[dup])) {
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496 dupidx <- which(gnames == dupname)
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497 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
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498 }
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499
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500 return (gnames)
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501 }
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502
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503 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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504 # https://github.com/sneumann/xcms/issues/247
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505 .concatenate_XCMSnExp <- function(...) {
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506 x <- list(...)
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507 if (length(x) == 0)
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508 return(NULL)
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509 if (length(x) == 1)
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510 return(x[[1]])
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511 ## Check that all are XCMSnExp objects.
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512 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
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513 stop("All passed objects should be 'XCMSnExp' objects")
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514 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
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515 ## If any of the XCMSnExp has alignment results or detected features drop
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516 ## them!
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517 x <- lapply(x, function(z) {
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518 if (hasAdjustedRtime(z)) {
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519 z <- dropAdjustedRtime(z)
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520 warning("Adjusted retention times found, had to drop them.")
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521 }
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522 if (hasFeatures(z)) {
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523 z <- dropFeatureDefinitions(z)
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524 warning("Feature definitions found, had to drop them.")
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525 }
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526 z
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527 })
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528 ## Combine peaks
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529 fls <- lapply(x, fileNames)
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530 startidx <- cumsum(lengths(fls))
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531 pks <- lapply(x, chromPeaks)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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532 procH <- lapply(x, processHistory)
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533 for (i in 2:length(fls)) {
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534 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
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535 procH[[i]] <- lapply(procH[[i]], function(z) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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536 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
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537 z
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538 })
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539 }
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540 pks <- do.call(rbind, pks)
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541 new_x@.processHistory <- unlist(procH)
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542 chromPeaks(new_x) <- pks
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543 if (validObject(new_x))
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544 new_x
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545 }
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546
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547 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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548 # https://github.com/sneumann/xcms/issues/247
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549 .concatenate_OnDiskMSnExp <- function(...) {
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550 x <- list(...)
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551 if (length(x) == 0)
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552 return(NULL)
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553 if (length(x) == 1)
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554 return(x[[1]])
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555 ## Check that all are XCMSnExp objects.
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556 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
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557 stop("All passed objects should be 'OnDiskMSnExp' objects")
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558 ## Check processingQueue
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559 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
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560 new_procQ <- procQ[[1]]
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561 is_ok <- unlist(lapply(procQ, function(z)
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562 !is.character(all.equal(new_procQ, z))
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563 ))
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564 if (any(!is_ok)) {
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565 warning("Processing queues from the submitted objects differ! ",
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566 "Dropping the processing queue.")
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567 new_procQ <- list()
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568 }
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569 ## processingData
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570 fls <- lapply(x, function(z) z@processingData@files)
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571 startidx <- cumsum(lengths(fls))
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572 ## featureData
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573 featd <- lapply(x, fData)
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574 ## Have to update the file index and the spectrum names.
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575 for (i in 2:length(featd)) {
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576 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
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577 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
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578 fileIds = featd[[i]]$fileIdx,
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579 spectrumIds = featd[[i]]$spIdx,
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580 nSpectra = nrow(featd[[i]]),
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581 nFiles = length(unlist(fls))
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582 )
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583 }
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584 featd <- do.call(rbind, featd)
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585 featd$spectrum <- 1:nrow(featd)
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586 ## experimentData
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587 expdata <- lapply(x, function(z) {
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588 ed <- z@experimentData
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589 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
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590 instrumentModel = ed@instrumentModel,
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591 ionSource = ed@ionSource,
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592 analyser = ed@analyser,
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593 detectorType = ed@detectorType,
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594 stringsAsFactors = FALSE)
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595 })
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596 expdata <- do.call(rbind, expdata)
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597 expdata <- new("MIAPE",
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598 instrumentManufacturer = expdata$instrumentManufacturer,
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599 instrumentModel = expdata$instrumentModel,
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600 ionSource = expdata$ionSource,
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601 analyser = expdata$analyser,
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602 detectorType = expdata$detectorType)
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603
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604 ## protocolData
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605 protodata <- lapply(x, function(z) z@protocolData)
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606 if (any(unlist(lapply(protodata, nrow)) > 0))
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607 warning("Found non-empty protocol data, but merging protocol data is",
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608 " currently not supported. Skipped.")
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609 ## phenoData
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610 pdata <- do.call(rbind, lapply(x, pData))
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611 res <- new(
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612 "OnDiskMSnExp",
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613 phenoData = new("NAnnotatedDataFrame", data = pdata),
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614 featureData = new("AnnotatedDataFrame", featd),
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615 processingData = new("MSnProcess",
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616 processing = paste0("Concatenated [", date(), "]"),
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617 files = unlist(fls), smoothed = NA),
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618 experimentData = expdata,
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619 spectraProcessingQueue = new_procQ)
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620 if (validObject(res))
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621 res
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622 }
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623
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624 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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625 # https://github.com/sneumann/xcms/issues/247
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626 c.XCMSnExp <- function(...) {
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627 .concatenate_XCMSnExp(...)
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628 }
34
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629
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630 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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631 # https://github.com/sneumann/xcms/issues/247
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632 c.MSnbase <- function(...) {
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633 .concatenate_OnDiskMSnExp(...)
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634 }