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annotate lib.r @ 32:b02d1992a43a draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 16:47:14 +0000
parents eb15a3841da4
children f5d51091cf84
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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4 #@author G. Le Corguille
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lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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6 parseCommandArgs <- function(...) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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7 args <- batch::parseCommandArgs(...)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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8 for (key in names(args)) {
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b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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9 if (args[key] %in% c("TRUE", "FALSE"))
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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10 args[key] <- as.logical(args[key])
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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11 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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12 return(args)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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13 }
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0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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14
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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15 #@author G. Le Corguille
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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16 # This function will
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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17 # - load the packages
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lecorguille
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18 # - display the sessionInfo
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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22 sessioninfo <- sessionInfo()
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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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$otherPkgs)) {
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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27 }
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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28 cat("\n")
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29 cat("Other loaded packages:\n")
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30 for (pkg in names(sessioninfo$loadedOnly)) {
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workflow4metabolomics
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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32 }
b02d1992a43a "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 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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36 #@author G. Le Corguille
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lecorguille
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37 # This function merge several chromBPI or chromTIC into one.
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lecorguille
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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)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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41 return(chrom_merged)
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42 }
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91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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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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lecorguille
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46 mergeXData <- function(args) {
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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47 chromTIC <- NULL
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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48 chromBPI <- NULL
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lecorguille
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49 chromTIC_adjusted <- NULL
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50 chromBPI_adjusted <- NULL
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workflow4metabolomics
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51 md5sumList <- NULL
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52 for (image in args$images) {
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lecorguille
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54 load(image)
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lecorguille
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55 # Handle infiles
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lecorguille
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56 if (!exists("singlefile")) singlefile <- NULL
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57 if (!exists("zipfile")) zipfile <- NULL
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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59 zipfile <- rawFilePath$zipfile
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lecorguille
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60 singlefile <- rawFilePath$singlefile
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lecorguille
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62 if (exists("raw_data")) xdata <- raw_data
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lecorguille
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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lecorguille
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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
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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71 sampleNamesList_merged <- sampleNamesList
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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72 chromTIC_merged <- chromTIC
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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73 chromBPI_merged <- chromBPI
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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76 } else {
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workflow4metabolomics
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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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")
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80
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workflow4metabolomics
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81 singlefile_merged <- c(singlefile_merged, singlefile)
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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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)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 12
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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89 }
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lecorguille
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90 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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91 rm(image)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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92 xdata <- xdata_merged; rm(xdata_merged)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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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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diff changeset
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
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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)]])) {
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372 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
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373 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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374
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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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377 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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378 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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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
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382 }
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workflow4metabolomics
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383 }
14b1c52fae62 "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
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388 # single
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389 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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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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workflow4metabolomics
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393 if (!file.exists(singlefile_galaxyPath)) {
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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 }
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diff changeset
397
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398 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))
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diff changeset
399 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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diff changeset
400 files <- c(files, singlefile_sampleName)
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lecorguille
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diff changeset
401 }
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lecorguille
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diff changeset
402 }
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diff changeset
403 # zipfile
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404 if (!is.null(zipfile) && (zipfile != "")) {
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workflow4metabolomics
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diff changeset
405 if (!file.exists(zipfile)) {
b02d1992a43a "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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diff changeset
406 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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lecorguille
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diff changeset
407 print(error_message)
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lecorguille
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diff changeset
408 stop(error_message)
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lecorguille
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diff changeset
409 }
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workflow4metabolomics
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diff changeset
410 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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lecorguille
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diff changeset
411
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
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diff changeset
412 #get the directory name
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workflow4metabolomics
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diff changeset
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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lecorguille
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diff changeset
415 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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lecorguille
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diff changeset
416 directory <- "."
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lecorguille
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diff changeset
417 if (length(directories) == 1) directory <- directories
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lecorguille
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diff changeset
418
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diff changeset
419 cat("files_root_directory\t", directory, "\n")
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lecorguille
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diff changeset
420
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workflow4metabolomics
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diff changeset
421 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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diff changeset
422 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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diff changeset
423 info <- file.info(directory)
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diff changeset
424 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
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diff changeset
425 files <- c(directory[!info$isdir], listed)
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diff changeset
426 exists <- file.exists(files)
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workflow4metabolomics
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diff changeset
427 files <- files[exists]
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workflow4metabolomics
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diff changeset
428
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lecorguille
parents: 11
diff changeset
429 }
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diff changeset
430 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
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workflow4metabolomics
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diff changeset
431
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lecorguille
parents:
diff changeset
432 }
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lecorguille
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diff changeset
433
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lecorguille
parents: 12
diff changeset
434
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lecorguille
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diff changeset
435 # This function retrieve a xset like object
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lecorguille
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diff changeset
436 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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lecorguille
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diff changeset
437 getxcmsSetObject <- function(xobject) {
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lecorguille
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diff changeset
438 # XCMS 1.x
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lecorguille
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diff changeset
439 if (class(xobject) == "xcmsSet")
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workflow4metabolomics
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diff changeset
440 return(xobject)
15
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lecorguille
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diff changeset
441 # XCMS 3.x
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lecorguille
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diff changeset
442 if (class(xobject) == "XCMSnExp") {
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lecorguille
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diff changeset
443 # Get the legacy xcmsSet object
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workflow4metabolomics
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diff changeset
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
parents: 12
diff changeset
447 else
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diff changeset
448 sampclass(xset) <- "."
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workflow4metabolomics
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diff changeset
449 return(xset)
15
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lecorguille
parents: 12
diff changeset
450 }
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff changeset
451 }