Mercurial > repos > lecorguille > xcms_export_samplemetadata

annotate lib.r @ 4:b3ecd79c8221 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Fri, 08 Feb 2019 10:08:21 -0500
parents ea1d802632ab
children 99a8a4213c4d
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9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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1 #@authors ABiMS TEAM, Y. Guitton
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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3
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4 #@author G. Le Corguille
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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6 parseCommandArgs <- function(...) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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7 args <- batch::parseCommandArgs(...)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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8 for (key in names(args)) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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9 if (args[key] %in% c("TRUE","FALSE"))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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10 args[key] = as.logical(args[key])
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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11 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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12 return(args)
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13 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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15 #@author G. Le Corguille
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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16 # This function will
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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17 # - load the packages
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18 # - display the sessionInfo
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19 loadAndDisplayPackages <- function(pkgs) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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22 sessioninfo = sessionInfo()
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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23 cat(sessioninfo$R.version$version.string,"\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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24 cat("Main packages:\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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26 cat("Other loaded packages:\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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28 }
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30 #@author G. Le Corguille
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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31 # This function merge several chromBPI or chromTIC into one.
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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32 mergeChrom <- function(chrom_merged, chrom) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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33 if (is.null(chrom_merged)) return(NULL)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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35 return(chrom_merged)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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36 }
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38 #@author G. Le Corguille
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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39 # This function merge several xdata into one.
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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40 mergeXData <- function(args) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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41 chromTIC <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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42 chromBPI <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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43 chromTIC_adjusted <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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44 chromBPI_adjusted <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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45 for(image in args$images) {
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46
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47 load(image)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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48 # Handle infiles
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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49 if (!exists("singlefile")) singlefile <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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50 if (!exists("zipfile")) zipfile <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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52 zipfile <- rawFilePath$zipfile
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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53 singlefile <- rawFilePath$singlefile
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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55
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56 if (exists("raw_data")) xdata <- raw_data
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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58
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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61 if (!exists("xdata_merged")) {
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62 xdata_merged <- xdata
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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63 singlefile_merged <- singlefile
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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64 md5sumList_merged <- md5sumList
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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65 sampleNamesList_merged <- sampleNamesList
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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66 chromTIC_merged <- chromTIC
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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67 chromBPI_merged <- chromBPI
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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83 }
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84 }
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85 rm(image)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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86 xdata <- xdata_merged; rm(xdata_merged)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 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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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
0
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
0
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 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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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
3
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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203
0
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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206
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207 }
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208
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209 #@author G. Le Corguille
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210 # It allow different of field separators
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211 getDataFrameFromFile <- function(filename, header=T) {
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) {
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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217 print(error_message)
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218 stop(error_message)
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219 }
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220 return(myDataFrame)
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221 }
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222
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223 #@author G. Le Corguille
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224 # Draw the BPI and TIC graphics
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225 # colored by sample names or class names
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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227
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228 if (aggregationFun == "sum")
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229 type="Total Ion Chromatograms"
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230 else
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231 type="Base Peak Intensity Chromatograms"
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232
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233 adjusted="Raw"
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234 if (hasAdjustedRtime(xdata))
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235 adjusted="Adjusted"
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236
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237 main <- paste(type,":",adjusted,"data")
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238
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239 pdf(pdfname, width=16, height=10)
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240
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241 # Color by group
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
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243 if (length(group_colors) > 1) {
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244 names(group_colors) <- unique(xdata$sample_group)
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main)
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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247 }
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248
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249 # Color by sample
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
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251 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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252
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253 dev.off()
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254 }
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255
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256
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257 # Get the polarities from all the samples of a condition
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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261 cat("Creating the sampleMetadata file...\n")
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262
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263 #Create the sampleMetada dataframe
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264 sampleMetadata <- xdata@phenoData@data
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265 rownames(sampleMetadata) <- NULL
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266 colnames(sampleMetadata) <- c("sample_name", "class")
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267
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268 sampleNamesOrigin <- sampleMetadata$sample_name
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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270
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271 if (any(duplicated(sampleNamesMakeNames))) {
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272 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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273 for (sampleName in sampleNamesOrigin) {
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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275 }
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276 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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277 }
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278
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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280 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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281 for (sampleName in sampleNamesOrigin) {
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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283 }
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284 }
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285
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286 sampleMetadata$sample_name <- sampleNamesMakeNames
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287
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288
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289 #For each sample file, the following actions are done
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290 for (fileIdx in 1:length(fileNames(xdata))) {
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291 #Check if the file is in the CDF format
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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293
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294 # If the column isn't exist, with add one filled with NA
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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296
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297 #Extract the polarity (a list of polarities)
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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299 #Verify if all the scans have the same polarity
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300 uniq_list <- unique(polarity)
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301 if (length(uniq_list)>1){
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302 polarity <- "mixed"
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303 } else {
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304 polarity <- as.character(uniq_list)
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305 }
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306
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307 #Set the polarity attribute
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308 sampleMetadata$polarity[fileIdx] <- polarity
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309 }
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310
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311 }
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312
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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314
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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316
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317 }
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318
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319
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320 # This function check if xcms will found all the files
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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322 checkFilesCompatibilityWithXcms <- function(directory) {
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323 cat("Checking files filenames compatibilities with xmcs...\n")
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324 # WHAT XCMS WILL FIND
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325 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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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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327 info <- file.info(directory)
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
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329 files <- c(directory[!info$isdir], listed)
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330 files_abs <- file.path(getwd(), files)
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331 exists <- file.exists(files_abs)
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332 files[exists] <- files_abs[exists]
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333 files[exists] <- sub("//","/",files[exists])
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334
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335 # WHAT IS ON THE FILESYSTEM
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336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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338
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339 # COMPARISON
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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343 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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344 }
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345 }
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346
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347
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348 #This function list the compatible files within the directory as xcms did
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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350 getMSFiles <- function (directory) {
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351 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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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
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353 info <- file.info(directory)
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
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355 files <- c(directory[!info$isdir], listed)
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356 exists <- file.exists(files)
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357 files <- files[exists]
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358 return(files)
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359 }
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360
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361 # This function check if XML contains special caracters. It also checks integrity and completness.
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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363 checkXmlStructure <- function (directory) {
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364 cat("Checking XML structure...\n")
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365
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366 cmd <- paste0("IFS=$'\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;")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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367 capture <- system(cmd, intern=TRUE)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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368
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
369 if (length(capture)>0){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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372 write(capture, stderr())
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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374 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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375
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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376 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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diff changeset
377
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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378
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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379 # This function check if XML contain special characters
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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381 deleteXmlBadCharacters<- function (directory) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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382 cat("Checking Non ASCII characters in the XML...\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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383
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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384 processed <- F
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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385 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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386 for (i in l){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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388 capture <- suppressWarnings(system(cmd, intern=TRUE))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
389 if (length(capture)>0){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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392 c <- system(cmd, intern=TRUE)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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393 capture <- ""
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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394 processed <- T
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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395 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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396 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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397 if (processed) cat("\n\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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398 return(processed)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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399 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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400
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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401
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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402 # This function will compute MD5 checksum to check the data integrity
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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404 getMd5sum <- function (directory) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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405 cat("Compute md5 checksum...\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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406 # WHAT XCMS WILL FIND
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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407 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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409 info <- file.info(directory)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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411 files <- c(directory[!info$isdir], listed)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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412 exists <- file.exists(files)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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413 files <- files[exists]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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414
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
415 library(tools)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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416
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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417 #cat("\n\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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418
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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419 return(as.matrix(md5sum(files)))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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420 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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diff changeset
421
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lecorguille
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422
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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423 # This function get the raw file path from the arguments
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
427
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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diff changeset
429
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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433 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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434 if (exists("singlefile_galaxyPaths")){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
437
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
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438 singlefile <- NULL
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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442 # In case, an url is used to import data within Galaxy
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
445 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
446 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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diff changeset
447 return(list(zipfile=zipfile, singlefile=singlefile))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
448 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
449
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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450 # This function retrieve the raw file in the working directory
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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451 # - if zipfile: unzip the file with its directory tree
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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452 # - if singlefiles: set symlink with the good filename
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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455 if(!is.null(singlefile) && (length("singlefile")>0)) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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456 for (singlefile_sampleName in names(singlefile)) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
458 if(!file.exists(singlefile_galaxyPath)){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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460 print(error_message); stop(error_message)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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461 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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462
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
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464 file.copy(singlefile_galaxyPath, singlefile_sampleName)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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465
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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466 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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467 directory <- "."
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
468
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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469 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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470 if(!is.null(zipfile) && (zipfile != "")) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
471 if(!file.exists(zipfile)){
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
473 print(error_message)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
474 stop(error_message)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
475 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
476
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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477 #list all file in the zip file
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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478 #zip_files <- unzip(zipfile,list=T)[,"Name"]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
479
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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480 #unzip
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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481 suppressWarnings(unzip(zipfile, unzip="unzip"))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
482
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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483 #get the directory name
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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484 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
487 directory <- "."
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
488 if (length(directories) == 1) directory <- directories
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
489
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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490 cat("files_root_directory\t",directory,"\n")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
491
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
492 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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493 return (directory)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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494 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
495
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
496
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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497 # This function retrieve a xset like object
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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499 getxcmsSetObject <- function(xobject) {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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500 # XCMS 1.x
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
501 if (class(xobject) == "xcmsSet")
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
502 return (xobject)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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503 # XCMS 3.x
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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504 if (class(xobject) == "XCMSnExp") {
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
505 # Get the legacy xcmsSet object
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
506 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
507 if (!is.null(xset@phenoData$sample_group))
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
508 sampclass(xset) <- xset@phenoData$sample_group
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
509 else
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
510 sampclass(xset) <- "."
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
diff changeset
511 return (xset)
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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512 }
9e8e5e1683a8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
lecorguille
parents:
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513 }