Mercurial > repos > lecorguille > xcms_fillpeaks

annotate lib.r @ 46:871ffc15a6da draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:52:02 +0000
parents 1a711c1b8b1f
children 1241183c8ae0
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
8fd5b5afa24d 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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f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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3
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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4 #@author G. Le Corguille
8fd5b5afa24d 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
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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6 parseCommandArgs <- function(...) {
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871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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7 args <- batch::parseCommandArgs(...)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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8 for (key in names(args)) {
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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9 if (args[key] %in% c("TRUE", "FALSE"))
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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10 args[key] <- as.logical(args[key])
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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11 }
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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12 return(args)
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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13 }
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f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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1c78d61fd646 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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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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16 # This function will
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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17 # - load the packages
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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18 # - display the sessionInfo
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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19 loadAndDisplayPackages <- function(pkgs) {
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871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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22 sessioninfo <- sessionInfo()
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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23 cat(sessioninfo$R.version$version.string, "\n")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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24 cat("Main packages:\n")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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25 for (pkg in names(sessioninfo$otherPkgs)) {
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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26 cat(paste(pkg, packageVersion(pkg)), "\t")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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27 }
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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28 cat("\n")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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29 cat("Other loaded packages:\n")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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30 for (pkg in names(sessioninfo$loadedOnly)) {
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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31 cat(paste(pkg, packageVersion(pkg)), "\t")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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32 }
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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33 cat("\n")
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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34 }
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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36 #@author G. Le Corguille
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e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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37 # This function merge several chromBPI or chromTIC into one.
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9eefb022a189 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
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38 mergeChrom <- function(chrom_merged, chrom) {
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39 if (is.null(chrom_merged)) return(NULL)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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41 return(chrom_merged)
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42 }
e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
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e67cbb96d9e9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
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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.
d8bac1291473 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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46 mergeXData <- function(args) {
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871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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47 chromTIC <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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48 chromBPI <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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49 chromTIC_adjusted <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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50 chromBPI_adjusted <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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51 md5sumList <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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52 for (image in args$images) {
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53
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54 load(image)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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55 # Handle infiles
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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56 if (!exists("singlefile")) singlefile <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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57 if (!exists("zipfile")) zipfile <- NULL
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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59 zipfile <- rawFilePath$zipfile
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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60 singlefile <- rawFilePath$singlefile
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62 if (exists("raw_data")) xdata <- raw_data
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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64
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65 cat(sampleNamesList$sampleNamesOrigin, "\n")
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66
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67 if (!exists("xdata_merged")) {
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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68 xdata_merged <- xdata
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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69 singlefile_merged <- singlefile
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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70 md5sumList_merged <- md5sumList
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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71 sampleNamesList_merged <- sampleNamesList
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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72 chromTIC_merged <- chromTIC
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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73 chromBPI_merged <- chromBPI
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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74 chromTIC_adjusted_merged <- chromTIC_adjusted
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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75 chromBPI_adjusted_merged <- chromBPI_adjusted
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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76 } else {
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
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80
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81 singlefile_merged <- c(singlefile_merged, singlefile)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
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89 }
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90 }
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91 rm(image)
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92 xdata <- xdata_merged
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93 rm(xdata_merged)
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94 singlefile <- singlefile_merged
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95 rm(singlefile_merged)
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96 md5sumList <- md5sumList_merged
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97 rm(md5sumList_merged)
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98 sampleNamesList <- sampleNamesList_merged
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99 rm(sampleNamesList_merged)
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100
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101 if (!is.null(args$sampleMetadata)) {
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102 cat("\tXSET PHENODATA SETTING...\n")
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103 sampleMetadataFile <- args$sampleMetadata
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104 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
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105 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
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106
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107 if (any(is.na(pData(xdata)$sample_group))) {
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108 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
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109 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
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110 print(error_message)
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111 stop(error_message)
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112 }
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113 }
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114
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115 if (!is.null(chromTIC_merged)) {
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116 chromTIC <- chromTIC_merged
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117 chromTIC@phenoData <- xdata@phenoData
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118 }
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119 if (!is.null(chromBPI_merged)) {
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120 chromBPI <- chromBPI_merged
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121 chromBPI@phenoData <- xdata@phenoData
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122 }
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123 if (!is.null(chromTIC_adjusted_merged)) {
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124 chromTIC_adjusted <- chromTIC_adjusted_merged
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125 chromTIC_adjusted@phenoData <- xdata@phenoData
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126 }
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127 if (!is.null(chromBPI_adjusted_merged)) {
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128 chromBPI_adjusted <- chromBPI_adjusted_merged
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129 chromBPI_adjusted@phenoData <- xdata@phenoData
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130 }
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131
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132 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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133 }
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134
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135 #@author G. Le Corguille
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136 # This function convert if it is required the Retention Time in minutes
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137 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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138 if (convertRTMinute) {
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139 #converting the retention times (seconds) into minutes
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140 print("converting the retention times into minutes in the variableMetadata")
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141 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
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142 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
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143 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
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144 }
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145 return(variableMetadata)
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146 }
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147
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148 #@author G. Le Corguille
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149 # This function format ions identifiers
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150 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
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151 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
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152 idsDeco <- sapply(splitDeco,
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153 function(x) {
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154 deco <- unlist(x)[2]
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155 if (is.na(deco)) return("") else return(paste0("_", deco))
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156 }
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157 )
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158 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
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159 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
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160 return(variableMetadata)
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161 }
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162
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163 #@author G. Le Corguille
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164 # This function convert the remain NA to 0 in the dataMatrix
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165 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
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166 if (naTOzero) {
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167 dataMatrix[is.na(dataMatrix)] <- 0
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168 }
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169 return(dataMatrix)
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170 }
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171
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172 #@author G. Le Corguille
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173 # Draw the plotChromPeakDensity 3 per page in a pdf file
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174 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
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175 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
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176
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177 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
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178
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179 if (length(unique(xdata$sample_group)) < 10) {
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180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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181 } else {
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182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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183 }
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184 names(group_colors) <- unique(xdata$sample_group)
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185 col_per_samp <- as.character(xdata$sample_group)
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186 for (i in seq_len(length(group_colors))) {
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187 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
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188 }
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189
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190 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
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191 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
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192 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
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193 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
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194 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
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195 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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196 }
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197
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198 dev.off()
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199 }
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200
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201 #@author G. Le Corguille
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202 # Draw the plotChromPeakDensity 3 per page in a pdf file
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203 getPlotAdjustedRtime <- function(xdata) {
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204
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205 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
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206
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207 # Color by group
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208 if (length(unique(xdata$sample_group)) < 10) {
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209 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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210 } else {
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211 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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212 }
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213 if (length(group_colors) > 1) {
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214 names(group_colors) <- unique(xdata$sample_group)
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215 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
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216 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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217 }
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218
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219 # Color by sample
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220 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
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221 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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222
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223 dev.off()
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224 }
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225
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226 #@author G. Le Corguille
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227 # value: intensity values to be used into, maxo or intb
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228 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
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229 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
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230 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
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231 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
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232 variableMetadata <- featureDefinitions(xdata)
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233 colnames(variableMetadata)[1] <- "mz"
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234 colnames(variableMetadata)[4] <- "rt"
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235 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
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236
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237 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
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238 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
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239 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
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240
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241 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
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242 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
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243
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244 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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245 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
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246
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247 }
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248
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249 #@author G. Le Corguille
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250 # It allow different of field separators
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251 getDataFrameFromFile <- function(filename, header = TRUE) {
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252 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
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253 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
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254 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
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255 if (ncol(myDataFrame) < 2) {
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256 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
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257 print(error_message)
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258 stop(error_message)
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259 }
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260 return(myDataFrame)
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261 }
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262
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263 #@author G. Le Corguille
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264 # Draw the BPI and TIC graphics
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265 # colored by sample names or class names
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1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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266 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
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267
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268 if (aggregationFun == "sum")
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269 type <- "Total Ion Chromatograms"
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270 else
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271 type <- "Base Peak Intensity Chromatograms"
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272
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273 adjusted <- "Raw"
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274 if (hasAdjustedRtime(xdata))
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275 adjusted <- "Adjusted"
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276
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277 main <- paste(type, ":", adjusted, "data")
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278
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279 pdf(pdfname, width = 16, height = 10)
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280
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281 # Color by group
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282 if (length(unique(xdata$sample_group)) < 10) {
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283 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
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284 } else {
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285 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
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286 }
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287 if (length(group_colors) > 1) {
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288 names(group_colors) <- unique(xdata$sample_group)
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289 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
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290 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
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291 }
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292
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293 # Color by sample
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294 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
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295 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
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296
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297 dev.off()
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298 }
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299
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300
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301 # Get the polarities from all the samples of a condition
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302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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1a711c1b8b1f "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
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305 cat("Creating the sampleMetadata file...\n")
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306
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307 #Create the sampleMetada dataframe
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308 sampleMetadata <- xdata@phenoData@data
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309 rownames(sampleMetadata) <- NULL
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310 colnames(sampleMetadata) <- c("sample_name", "class")
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311
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312 sampleNamesOrigin <- sampleMetadata$sample_name
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313 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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314
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315 if (any(duplicated(sampleNamesMakeNames))) {
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316 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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317 for (sampleName in sampleNamesOrigin) {
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318 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
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319 }
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320 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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321 }
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322
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323 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
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324 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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325 for (sampleName in sampleNamesOrigin) {
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326 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
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327 }
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328 }
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329
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330 sampleMetadata$sample_name <- sampleNamesMakeNames
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331
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332
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333 #For each sample file, the following actions are done
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334 for (fileIdx in seq_len(length(fileNames(xdata)))) {
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335 #Check if the file is in the CDF format
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336 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
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337
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338 # If the column isn't exist, with add one filled with NA
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339 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
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340
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341 #Extract the polarity (a list of polarities)
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342 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
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343 #Verify if all the scans have the same polarity
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344 uniq_list <- unique(polarity)
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345 if (length(uniq_list) > 1) {
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346 polarity <- "mixed"
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347 } else {
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348 polarity <- as.character(uniq_list)
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349 }
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350
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351 #Set the polarity attribute
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352 sampleMetadata$polarity[fileIdx] <- polarity
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353 }
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354
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355 }
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356
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357 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
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358
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359 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
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360
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361 }
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362
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363
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364 # This function will compute MD5 checksum to check the data integrity
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365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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366 getMd5sum <- function(files) {
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367 cat("Compute md5 checksum...\n")
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368 library(tools)
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369 return(as.matrix(md5sum(files)))
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370 }
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371
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372 # This function retrieve the raw file in the working directory
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373 # - if zipfile: unzip the file with its directory tree
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374 # - if singlefiles: set symlink with the good filename
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375 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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376 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
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377
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378 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
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379
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380 # single - if the file are passed in the command arguments -> refresh singlefile
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381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
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382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
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383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
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384
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385 singlefile <- NULL
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386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
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387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
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388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
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389 # In case, an url is used to import data within Galaxy
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390 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
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391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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392 }
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393 }
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394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
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395 if (!is.null(args[[paste0("zipfile", prefix)]]))
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396 zipfile <- args[[paste0("zipfile", prefix)]]
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397
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398 # single
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399 if (!is.null(singlefile) && (length("singlefile") > 0)) {
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400 files <- vector()
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401 for (singlefile_sampleName in names(singlefile)) {
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402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
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403 if (!file.exists(singlefile_galaxyPath)) {
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404 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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405 print(error_message)
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406 stop(error_message)
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407 }
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408
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409 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
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410 file.copy(singlefile_galaxyPath, singlefile_sampleName)
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411 files <- c(files, singlefile_sampleName)
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412 }
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413 }
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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414 # zipfile
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415 if (!is.null(zipfile) && (zipfile != "")) {
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416 if (!file.exists(zipfile)) {
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417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
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418 print(error_message)
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419 stop(error_message)
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420 }
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421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
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422
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423 #get the directory name
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424 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
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425 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
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426 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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427 directory <- "."
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428 if (length(directories) == 1) directory <- directories
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429
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430 cat("files_root_directory\t", directory, "\n")
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431
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432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
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434 info <- file.info(directory)
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435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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436 files <- c(directory[!info$isdir], listed)
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437 exists <- file.exists(files)
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438 files <- files[exists]
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439
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440 }
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441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
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442 }
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443
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444
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445 # This function retrieve a xset like object
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446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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447 getxcmsSetObject <- function(xobject) {
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448 # XCMS 1.x
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449 if (class(xobject) == "xcmsSet")
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450 return(xobject)
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451 # XCMS 3.x
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452 if (class(xobject) == "XCMSnExp") {
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453 # Get the legacy xcmsSet object
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454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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diff changeset
455 if (!is.null(xset@phenoData$sample_group))
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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diff changeset
456 sampclass(xset) <- xset@phenoData$sample_group
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 45
diff changeset
457 else
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
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diff changeset
458 sampclass(xset) <- "."
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 45
diff changeset
459 return(xset)
871ffc15a6da planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 45
diff changeset
460 }
31
8fd5b5afa24d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 30
diff changeset
461 }