Mercurial > repos > lecorguille > xcms_xcmsset

annotate lib.r @ 50:1c63d9d402e6 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 10:33:00 +0000
parents d4a0eed3099d
children 44ab040fffa0
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
2bf1cb023c94 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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3
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
2bf1cb023c94 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
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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8 for (key in names(args)) {
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1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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9 if (args[key] %in% c("TRUE", "FALSE"))
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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10 args[key] <- as.logical(args[key])
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lecorguille
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11 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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12 return(args)
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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13 }
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f28041d2180a 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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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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16 # This function will
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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19 loadAndDisplayPackages <- function(pkgs) {
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20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
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1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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22 sessioninfo <- sessionInfo()
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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23 cat(sessioninfo$R.version$version.string, "\n")
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24 cat("Main packages:\n")
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25 for (pkg in names(sessioninfo$otherPkgs)) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
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27 }
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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28 cat("\n")
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29 cat("Other loaded packages:\n")
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30 for (pkg in names(sessioninfo$loadedOnly)) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
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32 }
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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33 cat("\n")
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lecorguille
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34 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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36 #@author G. Le Corguille
36
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37 # This function merge several chromBPI or chromTIC into one.
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38 mergeChrom <- function(chrom_merged, chrom) {
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lecorguille
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39 if (is.null(chrom_merged)) return(NULL)
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lecorguille
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
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41 return(chrom_merged)
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42 }
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44 #@author G. Le Corguille
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lecorguille
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45 # This function merge several xdata into one.
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46 mergeXData <- function(args) {
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47 chromTIC <- NULL
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lecorguille
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48 chromBPI <- NULL
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49 chromTIC_adjusted <- NULL
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50 chromBPI_adjusted <- NULL
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51 md5sumList <- NULL
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52 for (image in args$images) {
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53
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54 load(image)
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lecorguille
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55 # Handle infiles
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lecorguille
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56 if (!exists("singlefile")) singlefile <- NULL
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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60 singlefile <- rawFilePath$singlefile
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61
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62 if (exists("raw_data")) xdata <- raw_data
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
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68 xdata_merged <- xdata
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lecorguille
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69 singlefile_merged <- singlefile
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lecorguille
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70 md5sumList_merged <- md5sumList
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71 sampleNamesList_merged <- sampleNamesList
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lecorguille
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72 chromTIC_merged <- chromTIC
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73 chromBPI_merged <- chromBPI
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
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lecorguille
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
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76 } else {
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
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79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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80
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81 singlefile_merged <- c(singlefile_merged, singlefile)
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
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lecorguille
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
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lecorguille
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
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lecorguille
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
e66eeca443e4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
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91 rm(image)
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92 xdata <- xdata_merged; rm(xdata_merged)
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93 singlefile <- singlefile_merged; rm(singlefile_merged)
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94 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
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95 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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96
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97 if (!is.null(args$sampleMetadata)) {
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98 cat("\tXSET PHENODATA SETTING...\n")
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99 sampleMetadataFile <- args$sampleMetadata
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100 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = F)
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101 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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102
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103 if (any(is.na(pData(xdata)$sample_group))) {
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104 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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105 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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106 print(error_message)
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107 stop(error_message)
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108 }
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109 }
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110
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111 if (!is.null(chromTIC_merged)) {
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112 chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData
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113 }
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114 if (!is.null(chromBPI_merged)) {
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115 chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData
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116 }
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117 if (!is.null(chromTIC_adjusted_merged)) {
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118 chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData
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119 }
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120 if (!is.null(chromBPI_adjusted_merged)) {
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121 chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData
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122 }
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123
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124 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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125 }
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126
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127 #@author G. Le Corguille
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128 # This function convert if it is required the Retention Time in minutes
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129 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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130 if (convertRTMinute) {
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131 #converting the retention times (seconds) into minutes
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132 print("converting the retention times into minutes in the variableMetadata")
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133 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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134 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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135 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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136 }
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137 return(variableMetadata)
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138 }
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139
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140 #@author G. Le Corguille
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141 # This function format ions identifiers
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142 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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143 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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144 idsDeco <- sapply(splitDeco,
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145 function(x) {
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146 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
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147 }
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148 )
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149 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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150 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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151 return(variableMetadata)
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152 }
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153
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154 #@author G. Le Corguille
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155 # This function convert the remain NA to 0 in the dataMatrix
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156 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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157 if (naTOzero) {
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158 dataMatrix[is.na(dataMatrix)] <- 0
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159 }
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160 return(dataMatrix)
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161 }
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162
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163 #@author G. Le Corguille
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164 # Draw the plotChromPeakDensity 3 per page in a pdf file
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165 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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166 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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167
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168 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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169
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170 if (length(unique(xdata$sample_group)) < 10) {
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171 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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172 }else{
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173 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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174 }
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175 names(group_colors) <- unique(xdata$sample_group)
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176 col_per_samp <- as.character(xdata$sample_group)
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177 for (i in seq_len(length(group_colors))) {
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178 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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179 }
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180
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181 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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182 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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183 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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184 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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185 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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186 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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187 }
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188
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189 dev.off()
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190 }
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191
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192 #@author G. Le Corguille
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193 # Draw the plotChromPeakDensity 3 per page in a pdf file
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194 getPlotAdjustedRtime <- function(xdata) {
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195
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196 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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197
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198 # Color by group
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199 if (length(unique(xdata$sample_group)) < 10) {
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200 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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201 } else {
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202 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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203 }
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204 if (length(group_colors) > 1) {
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205 names(group_colors) <- unique(xdata$sample_group)
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206 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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207 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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208 }
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209
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210 # Color by sample
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211 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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212 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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213
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214 dev.off()
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215 }
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216
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217 #@author G. Le Corguille
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218 # value: intensity values to be used into, maxo or intb
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219 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = F, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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220 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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221 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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222 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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223 variableMetadata <- featureDefinitions(xdata)
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224 colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt"
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225 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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226
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227 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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228 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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229 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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230
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231 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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232 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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233
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234 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = F, row.names = F)
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235 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = F, row.names = F)
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236
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237 }
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238
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239 #@author G. Le Corguille
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240 # It allow different of field separators
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241 getDataFrameFromFile <- function(filename, header = T) {
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242 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = F)
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243 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = F)
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244 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = F)
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245 if (ncol(myDataFrame) < 2) {
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246 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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247 print(error_message)
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248 stop(error_message)
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249 }
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250 return(myDataFrame)
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251 }
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252
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253 #@author G. Le Corguille
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254 # Draw the BPI and TIC graphics
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255 # colored by sample names or class names
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256 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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257
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258 if (aggregationFun == "sum")
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259 type <- "Total Ion Chromatograms"
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260 else
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261 type <- "Base Peak Intensity Chromatograms"
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262
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263 adjusted <- "Raw"
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264 if (hasAdjustedRtime(xdata))
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265 adjusted <- "Adjusted"
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266
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267 main <- paste(type, ":", adjusted, "data")
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268
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269 pdf(pdfname, width = 16, height = 10)
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270
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271 # Color by group
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272 if (length(unique(xdata$sample_group)) < 10) {
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273 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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274 }else{
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275 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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276 }
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277 if (length(group_colors) > 1) {
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278 names(group_colors) <- unique(xdata$sample_group)
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279 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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280 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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281 }
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282
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283 # Color by sample
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284 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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285 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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286
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287 dev.off()
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288 }
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289
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290
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291 # Get the polarities from all the samples of a condition
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292 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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293 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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294 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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295 cat("Creating the sampleMetadata file...\n")
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296
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297 #Create the sampleMetada dataframe
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298 sampleMetadata <- xdata@phenoData@data
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299 rownames(sampleMetadata) <- NULL
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300 colnames(sampleMetadata) <- c("sample_name", "class")
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301
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302 sampleNamesOrigin <- sampleMetadata$sample_name
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303 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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304
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305 if (any(duplicated(sampleNamesMakeNames))) {
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306 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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307 for (sampleName in sampleNamesOrigin) {
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308 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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309 }
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310 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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311 }
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312
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313 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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314 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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315 for (sampleName in sampleNamesOrigin) {
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316 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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317 }
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318 }
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319
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320 sampleMetadata$sample_name <- sampleNamesMakeNames
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321
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322
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323 #For each sample file, the following actions are done
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324 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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325 #Check if the file is in the CDF format
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326 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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327
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328 # If the column isn't exist, with add one filled with NA
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329 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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330
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331 #Extract the polarity (a list of polarities)
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332 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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333 #Verify if all the scans have the same polarity
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334 uniq_list <- unique(polarity)
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335 if (length(uniq_list) > 1) {
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336 polarity <- "mixed"
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337 } else {
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338 polarity <- as.character(uniq_list)
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339 }
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340
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341 #Set the polarity attribute
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342 sampleMetadata$polarity[fileIdx] <- polarity
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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 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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348
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349 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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350
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351 }
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352
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353
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354 # This function will compute MD5 checksum to check the data integrity
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355 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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356 getMd5sum <- function(files) {
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357 cat("Compute md5 checksum...\n")
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358 library(tools)
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359 return(as.matrix(md5sum(files)))
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360 }
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361
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362 # This function retrieve the raw file in the working directory
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363 # - if zipfile: unzip the file with its directory tree
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364 # - if singlefiles: set symlink with the good filename
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365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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366 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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367
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368 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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369
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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370 # single - if the file are passed in the command arguments -> refresh singlefile
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371 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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372 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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373 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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374
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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375 singlefile <- NULL
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376 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
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b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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377 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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378 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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379 # In case, an url is used to import data within Galaxy
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380 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
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381 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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382 }
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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383 }
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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384 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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385 if (!is.null(args[[paste0("zipfile", prefix)]]))
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386 zipfile <- args[[paste0("zipfile", prefix)]]
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387
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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388 # single
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389 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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390 files <- vector()
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391 for (singlefile_sampleName in names(singlefile)) {
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392 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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393 if (!file.exists(singlefile_galaxyPath)) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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394 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
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395 print(error_message); stop(error_message)
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396 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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397
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398 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
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399 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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400 files <- c(files, singlefile_sampleName)
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lecorguille
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401 }
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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402 }
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403 # zipfile
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404 if (!is.null(zipfile) && (zipfile != "")) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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405 if (!file.exists(zipfile)) {
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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406 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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407 print(error_message)
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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408 stop(error_message)
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409 }
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410 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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411
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412 #get the directory name
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413 suppressWarnings(filesInZip <- unzip(zipfile, list = T))
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414 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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415 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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416 directory <- "."
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417 if (length(directories) == 1) directory <- directories
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418
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419 cat("files_root_directory\t", directory, "\n")
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420
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421 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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422 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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423 info <- file.info(directory)
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424 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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425 files <- c(directory[!info$isdir], listed)
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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426 exists <- file.exists(files)
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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427 files <- files[exists]
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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428
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lecorguille
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429 }
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430 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
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431
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lecorguille
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432 }
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433
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434
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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435 # This function retrieve a xset like object
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lecorguille
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436 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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437 getxcmsSetObject <- function(xobject) {
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lecorguille
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438 # XCMS 1.x
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439 if (class(xobject) == "xcmsSet")
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440 return(xobject)
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lecorguille
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441 # XCMS 3.x
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lecorguille
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442 if (class(xobject) == "XCMSnExp") {
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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443 # Get the legacy xcmsSet object
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444 suppressWarnings(xset <- as(xobject, "xcmsSet"))
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lecorguille
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diff changeset
445 if (!is.null(xset@phenoData$sample_group))
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lecorguille
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diff changeset
446 sampclass(xset) <- xset@phenoData$sample_group
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lecorguille
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diff changeset
447 else
9ada611dd63f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
448 sampclass(xset) <- "."
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workflow4metabolomics
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449 return(xset)
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lecorguille
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450 }
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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451 }