Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 46:32c1cbdbdd3b draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
author workflow4metabolomics
date Thu, 13 Feb 2020 11:42:41 +0000
parents 1986c48d86ce
children 08b09c2836cd
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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1 #@authors ABiMS TEAM, Y. Guitton
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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5 # solve an issue with batch if arguments are logical TRUE/FALSE
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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7 args <- batch::parseCommandArgs(...)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8 for (key in names(args)) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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9 if (args[key] %in% c("TRUE","FALSE"))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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10 args[key] = as.logical(args[key])
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lecorguille
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11 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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12 return(args)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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13 }
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c04568596f40 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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15 #@author G. Le Corguille
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16 # This function will
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
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lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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22 sessioninfo = sessionInfo()
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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23 cat(sessioninfo$R.version$version.string,"\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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24 cat("Main packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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26 cat("Other loaded packages:\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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28 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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lecorguille
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30 #@author G. Le Corguille
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lecorguille
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31 # This function merge several chromBPI or chromTIC into one.
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lecorguille
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32 mergeChrom <- function(chrom_merged, chrom) {
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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33 if (is.null(chrom_merged)) return(NULL)
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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35 return(chrom_merged)
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36 }
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lecorguille
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38 #@author G. Le Corguille
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lecorguille
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39 # This function merge several xdata into one.
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lecorguille
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40 mergeXData <- function(args) {
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lecorguille
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41 chromTIC <- NULL
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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42 chromBPI <- NULL
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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43 chromTIC_adjusted <- NULL
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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44 chromBPI_adjusted <- NULL
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1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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45 md5sumList <- NULL
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46 for(image in args$images) {
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48 load(image)
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lecorguille
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49 # Handle infiles
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lecorguille
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50 if (!exists("singlefile")) singlefile <- NULL
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51 if (!exists("zipfile")) zipfile <- NULL
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1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
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53 zipfile <- rawFilePath$zipfile
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54 singlefile <- rawFilePath$singlefile
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56 if (exists("raw_data")) xdata <- raw_data
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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59 cat(sampleNamesList$sampleNamesOrigin,"\n")
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60
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lecorguille
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61 if (!exists("xdata_merged")) {
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lecorguille
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62 xdata_merged <- xdata
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lecorguille
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63 singlefile_merged <- singlefile
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lecorguille
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64 md5sumList_merged <- md5sumList
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65 sampleNamesList_merged <- sampleNamesList
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lecorguille
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66 chromTIC_merged <- chromTIC
2b0a4c7a4a48 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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67 chromBPI_merged <- chromBPI
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lecorguille
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68 chromTIC_adjusted_merged <- chromTIC_adjusted
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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69 chromBPI_adjusted_merged <- chromBPI_adjusted
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70 } else {
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
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lecorguille
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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74
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75 singlefile_merged <- c(singlefile_merged,singlefile)
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lecorguille
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
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35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
35a20d7c9f33 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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83 }
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lecorguille
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84 }
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lecorguille
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85 rm(image)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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86 xdata <- xdata_merged; rm(xdata_merged)
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lecorguille
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87 singlefile <- singlefile_merged; rm(singlefile_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
9714270678a7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
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90
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91 if (!is.null(args$sampleMetadata)) {
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92 cat("\tXSET PHENODATA SETTING...\n")
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93 sampleMetadataFile <- args$sampleMetadata
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
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96
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97 if (any(is.na(pData(xdata)$sample_group))) {
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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100 print(error_message)
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101 stop(error_message)
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102 }
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103 }
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104
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
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109
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
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111 }
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112
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113 #@author G. Le Corguille
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114 # This function convert if it is required the Retention Time in minutes
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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116 if (convertRTMinute){
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117 #converting the retention times (seconds) into minutes
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118 print("converting the retention times into minutes in the variableMetadata")
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
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122 }
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123 return (variableMetadata)
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124 }
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125
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126 #@author G. Le Corguille
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127 # This function format ions identifiers
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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133 return(variableMetadata)
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134 }
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135
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136 #@author G. Le Corguille
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137 # This function convert the remain NA to 0 in the dataMatrix
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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139 if (naTOzero){
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140 dataMatrix[is.na(dataMatrix)] <- 0
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141 }
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142 return (dataMatrix)
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143 }
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144
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145 #@author G. Le Corguille
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file
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147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
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149
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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151
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152 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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153 names(group_colors) <- unique(xdata$sample_group)
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154
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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156 for (i in 1:nrow(featureDefinitions(xdata))) {
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax
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159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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161 }
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162
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163 dev.off()
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164 }
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165
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166 #@author G. Le Corguille
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file
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168 getPlotAdjustedRtime <- function(xdata) {
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169
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
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171
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172 # Color by group
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173 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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174 if (length(group_colors) > 1) {
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175 names(group_colors) <- unique(xdata$sample_group)
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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178 }
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179
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180 # Color by sample
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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183
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184 dev.off()
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185 }
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186
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187 #@author G. Le Corguille
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188 # value: intensity values to be used into, maxo or intb
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
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193 variableMetadata <- featureDefinitions(xdata)
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
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196
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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200
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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203
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
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206
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207 }
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208
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209 #@author G. Le Corguille
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210 # It allow different of field separators
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211 getDataFrameFromFile <- function(filename, header=T) {
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
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215 if (ncol(myDataFrame) < 2) {
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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217 print(error_message)
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218 stop(error_message)
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219 }
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220 return(myDataFrame)
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221 }
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222
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223 #@author G. Le Corguille
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224 # Draw the BPI and TIC graphics
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225 # colored by sample names or class names
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
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227
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228 if (aggregationFun == "sum")
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229 type="Total Ion Chromatograms"
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230 else
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231 type="Base Peak Intensity Chromatograms"
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232
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233 adjusted="Raw"
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234 if (hasAdjustedRtime(xdata))
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235 adjusted="Adjusted"
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236
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237 main <- paste(type,":",adjusted,"data")
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238
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239 pdf(pdfname, width=16, height=10)
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240
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241 # Color by group
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242 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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243 if (length(group_colors) > 1) {
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244 names(group_colors) <- unique(xdata$sample_group)
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245 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
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247 }
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248
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249 # Color by sample
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")
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251 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
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252
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253 dev.off()
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254 }
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255
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256
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257 # Get the polarities from all the samples of a condition
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
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261 cat("Creating the sampleMetadata file...\n")
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262
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263 #Create the sampleMetada dataframe
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264 sampleMetadata <- xdata@phenoData@data
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265 rownames(sampleMetadata) <- NULL
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266 colnames(sampleMetadata) <- c("sample_name", "class")
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267
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268 sampleNamesOrigin <- sampleMetadata$sample_name
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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270
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271 if (any(duplicated(sampleNamesMakeNames))) {
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272 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
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273 for (sampleName in sampleNamesOrigin) {
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
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275 }
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276 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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277 }
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278
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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280 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
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281 for (sampleName in sampleNamesOrigin) {
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
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283 }
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284 }
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285
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286 sampleMetadata$sample_name <- sampleNamesMakeNames
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287
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288
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289 #For each sample file, the following actions are done
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290 for (fileIdx in 1:length(fileNames(xdata))) {
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291 #Check if the file is in the CDF format
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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293
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294 # If the column isn't exist, with add one filled with NA
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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296
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297 #Extract the polarity (a list of polarities)
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
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299 #Verify if all the scans have the same polarity
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300 uniq_list <- unique(polarity)
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301 if (length(uniq_list)>1){
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302 polarity <- "mixed"
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303 } else {
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304 polarity <- as.character(uniq_list)
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305 }
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306
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307 #Set the polarity attribute
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308 sampleMetadata$polarity[fileIdx] <- polarity
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309 }
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310
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311 }
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312
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
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314
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
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316
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317 }
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318
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319
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320 # This function will compute MD5 checksum to check the data integrity
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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322 getMd5sum <- function (files) {
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323 cat("Compute md5 checksum...\n")
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324 library(tools)
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325 return(as.matrix(md5sum(files)))
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326 }
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327
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328 # This function retrieve the raw file in the working directory
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329 # - if zipfile: unzip the file with its directory tree
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330 # - if singlefiles: set symlink with the good filename
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331 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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332 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {
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333
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334 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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335
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336 # single - if the file are passed in the command arguments -> refresh singlefile
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337 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
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338 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\|"))
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339 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\|"))
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340
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341 singlefile <- NULL
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342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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345 # In case, an url is used to import data within Galaxy
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346 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
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347 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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348 }
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349 }
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350 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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351 if (!is.null(args[[paste0("zipfile",prefix)]]))
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352 zipfile <- args[[paste0("zipfile",prefix)]]
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353
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354 # single
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355 if(!is.null(singlefile) && (length("singlefile")>0)) {
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356 files <- vector()
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357 for (singlefile_sampleName in names(singlefile)) {
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358 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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359 if(!file.exists(singlefile_galaxyPath)){
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360 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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361 print(error_message); stop(error_message)
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362 }
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363
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364 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
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365 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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366 files <- c(files, singlefile_sampleName)
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367 }
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368 }
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369 # zipfile
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370 if(!is.null(zipfile) && (zipfile != "")) {
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411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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371 if(!file.exists(zipfile)){
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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372 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
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373 print(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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374 stop(error_message)
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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375 }
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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376 suppressWarnings(unzip(zipfile, unzip="unzip"))
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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377
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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378 #get the directory name
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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379 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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380 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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381 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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382 directory <- "."
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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383 if (length(directories) == 1) directory <- directories
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411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 19
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384
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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385 cat("files_root_directory\t",directory,"\n")
411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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386
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1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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387 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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388 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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389 info <- file.info(directory)
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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390 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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391 files <- c(directory[!info$isdir], listed)
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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392 exists <- file.exists(files)
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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393 files <- files[exists]
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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394
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411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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395 }
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1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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396 return(list(zipfile=zipfile, singlefile=singlefile, files=files))
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 43
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397
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411d2b9ea412 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
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398 }
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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399
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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400
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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401 # This function retrieve a xset like object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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402 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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403 getxcmsSetObject <- function(xobject) {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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404 # XCMS 1.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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405 if (class(xobject) == "xcmsSet")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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406 return (xobject)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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407 # XCMS 3.x
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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408 if (class(xobject) == "XCMSnExp") {
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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409 # Get the legacy xcmsSet object
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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410 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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e309e6af6744 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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411 if (!is.null(xset@phenoData$sample_group))
e309e6af6744 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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412 sampclass(xset) <- xset@phenoData$sample_group
e309e6af6744 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
lecorguille
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diff changeset
413 else
e309e6af6744 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
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414 sampclass(xset) <- "."
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
diff changeset
415 return (xset)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 29
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416 }
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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417 }