Mercurial > repos > lecorguille > msnbase_readmsdata
annotate lib.r @ 11:86a20118e743 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
author | lecorguille |
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date | Tue, 30 Apr 2019 04:40:33 -0400 |
parents | a874afcb71ca |
children | 226fb89cacc4 |
rev | line source |
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0
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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1 #@authors ABiMS TEAM, Y. Guitton |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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2 # lib.r for Galaxy Workflow4Metabolomics xcms tools |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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3 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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4 #@author G. Le Corguille |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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5 # solve an issue with batch if arguments are logical TRUE/FALSE |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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6 parseCommandArgs <- function(...) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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7 args <- batch::parseCommandArgs(...) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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8 for (key in names(args)) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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9 if (args[key] %in% c("TRUE","FALSE")) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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10 args[key] = as.logical(args[key]) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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11 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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12 return(args) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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13 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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14 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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15 #@author G. Le Corguille |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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16 # This function will |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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17 # - load the packages |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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18 # - display the sessionInfo |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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19 loadAndDisplayPackages <- function(pkgs) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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21 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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22 sessioninfo = sessionInfo() |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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23 cat(sessioninfo$R.version$version.string,"\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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24 cat("Main packages:\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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26 cat("Other loaded packages:\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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28 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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29 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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30 #@author G. Le Corguille |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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31 # This function merge several chromBPI or chromTIC into one. |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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32 mergeChrom <- function(chrom_merged, chrom) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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33 if (is.null(chrom_merged)) return(NULL) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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35 return(chrom_merged) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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36 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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37 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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38 #@author G. Le Corguille |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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39 # This function merge several xdata into one. |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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40 mergeXData <- function(args) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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41 chromTIC <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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42 chromBPI <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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43 chromTIC_adjusted <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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44 chromBPI_adjusted <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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45 for(image in args$images) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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46 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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47 load(image) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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48 # Handle infiles |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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49 if (!exists("singlefile")) singlefile <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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50 if (!exists("zipfile")) zipfile <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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52 zipfile <- rawFilePath$zipfile |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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53 singlefile <- rawFilePath$singlefile |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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55 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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56 if (exists("raw_data")) xdata <- raw_data |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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58 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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59 cat(sampleNamesList$sampleNamesOrigin,"\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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60 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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61 if (!exists("xdata_merged")) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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62 xdata_merged <- xdata |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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63 singlefile_merged <- singlefile |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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64 md5sumList_merged <- md5sumList |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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65 sampleNamesList_merged <- sampleNamesList |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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66 chromTIC_merged <- chromTIC |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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67 chromBPI_merged <- chromBPI |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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68 chromTIC_adjusted_merged <- chromTIC_adjusted |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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69 chromBPI_adjusted_merged <- chromBPI_adjusted |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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70 } else { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) |
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d7a7ef786fbe
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
lecorguille
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata) |
0
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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74 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 singlefile_merged <- c(singlefile_merged,singlefile) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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83 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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84 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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85 rm(image) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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86 xdata <- xdata_merged; rm(xdata_merged) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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87 singlefile <- singlefile_merged; rm(singlefile_merged) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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90 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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91 if (!is.null(args$sampleMetadata)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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92 cat("\tXSET PHENODATA SETTING...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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93 sampleMetadataFile <- args$sampleMetadata |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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96 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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97 if (any(is.na(pData(xdata)$sample_group))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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100 print(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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101 stop(error_message) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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102 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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103 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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104 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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109 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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111 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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112 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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113 #@author G. Le Corguille |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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114 # This function convert if it is required the Retention Time in minutes |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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116 if (convertRTMinute){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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117 #converting the retention times (seconds) into minutes |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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118 print("converting the retention times into minutes in the variableMetadata") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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122 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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123 return (variableMetadata) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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124 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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125 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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126 #@author G. Le Corguille |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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127 # This function format ions identifiers |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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133 return(variableMetadata) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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134 } |
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135 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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136 #@author G. Le Corguille |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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137 # This function convert the remain NA to 0 in the dataMatrix |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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139 if (naTOzero){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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140 dataMatrix[is.na(dataMatrix)] <- 0 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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141 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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142 return (dataMatrix) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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143 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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144 |
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145 #@author G. Le Corguille |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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151 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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153 names(group_colors) <- unique(xdata$sample_group) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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154 |
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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156 for (i in 1:nrow(featureDefinitions(xdata))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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158 mzmax = featureDefinitions(xdata)[i,]$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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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168 getPlotAdjustedRtime <- function(xdata) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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169 |
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) |
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171 |
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172 # Color by group |
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173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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174 if (length(group_colors) > 1) { |
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175 names(group_colors) <- unique(xdata$sample_group) |
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176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) |
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177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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178 } |
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179 |
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180 # Color by sample |
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181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) |
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182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) |
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183 |
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184 dev.off() |
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185 } |
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186 |
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187 #@author G. Le Corguille |
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188 # value: intensity values to be used into, maxo or intb |
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189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { |
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190 dataMatrix <- featureValues(xdata, method="medret", value=intval) |
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191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) |
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192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix) |
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193 variableMetadata <- featureDefinitions(xdata) |
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194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" |
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195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) |
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196 |
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197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) |
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198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) |
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200 |
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201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export |
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202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",") |
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203 |
0
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204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
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205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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206 |
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207 } |
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208 |
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209 #@author G. Le Corguille |
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210 # It allow different of field separators |
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211 getDataFrameFromFile <- function(filename, header=T) { |
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212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) |
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213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) |
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214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) |
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215 if (ncol(myDataFrame) < 2) { |
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216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" |
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217 print(error_message) |
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218 stop(error_message) |
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219 } |
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220 return(myDataFrame) |
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221 } |
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222 |
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223 #@author G. Le Corguille |
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224 # Draw the BPI and TIC graphics |
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225 # colored by sample names or class names |
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226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { |
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227 |
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228 if (aggregationFun == "sum") |
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229 type="Total Ion Chromatograms" |
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230 else |
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231 type="Base Peak Intensity Chromatograms" |
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232 |
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233 adjusted="Raw" |
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234 if (hasAdjustedRtime(xdata)) |
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235 adjusted="Adjusted" |
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236 |
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237 main <- paste(type,":",adjusted,"data") |
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238 |
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239 pdf(pdfname, width=16, height=10) |
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240 |
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241 # Color by group |
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242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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243 if (length(group_colors) > 1) { |
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244 names(group_colors) <- unique(xdata$sample_group) |
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245 plot(chrom, col = group_colors[chrom$sample_group], main=main) |
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246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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247 } |
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248 |
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249 # Color by sample |
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250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main) |
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251 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) |
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252 |
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253 dev.off() |
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254 } |
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255 |
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256 |
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257 # Get the polarities from all the samples of a condition |
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258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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261 cat("Creating the sampleMetadata file...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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262 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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263 #Create the sampleMetada dataframe |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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264 sampleMetadata <- xdata@phenoData@data |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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265 rownames(sampleMetadata) <- NULL |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
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266 colnames(sampleMetadata) <- c("sample_name", "class") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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267 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
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268 sampleNamesOrigin <- sampleMetadata$sample_name |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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269 sampleNamesMakeNames <- make.names(sampleNamesOrigin) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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270 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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271 if (any(duplicated(sampleNamesMakeNames))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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273 for (sampleName in sampleNamesOrigin) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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275 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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277 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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278 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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281 for (sampleName in sampleNamesOrigin) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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283 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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284 } |
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285 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
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286 sampleMetadata$sample_name <- sampleNamesMakeNames |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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290 for (fileIdx in 1:length(fileNames(xdata))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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291 #Check if the file is in the CDF format |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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292 if (!mzR:::netCDFIsFile(fileNames(xdata))) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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293 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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294 # If the column isn't exist, with add one filled with NA |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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296 |
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297 #Extract the polarity (a list of polarities) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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299 #Verify if all the scans have the same polarity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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300 uniq_list <- unique(polarity) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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301 if (length(uniq_list)>1){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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302 polarity <- "mixed" |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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303 } else { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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304 polarity <- as.character(uniq_list) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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305 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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306 |
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307 #Set the polarity attribute |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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308 sampleMetadata$polarity[fileIdx] <- polarity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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309 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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310 |
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311 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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312 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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314 |
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315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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316 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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317 } |
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318 |
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319 |
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320 # This function check if xcms will found all the files |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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322 checkFilesCompatibilityWithXcms <- function(directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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323 cat("Checking files filenames compatibilities with xmcs...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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324 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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325 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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327 info <- file.info(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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329 files <- c(directory[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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330 files_abs <- file.path(getwd(), files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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331 exists <- file.exists(files_abs) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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332 files[exists] <- files_abs[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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333 files[exists] <- sub("//","/",files[exists]) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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334 |
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335 # WHAT IS ON THE FILESYSTEM |
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336 filesystem_filepaths <- system(paste0("find \"",getwd(),"/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) |
0
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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338 |
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339 # COMPARISON |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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343 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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344 } |
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345 } |
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346 |
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347 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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348 #This function list the compatible files within the directory as xcms did |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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350 getMSFiles <- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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351 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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353 info <- file.info(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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355 files <- c(directory[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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356 exists <- file.exists(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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357 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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358 return(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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359 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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360 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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361 # This function check if XML contains special caracters. It also checks integrity and completness. |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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363 checkXmlStructure <- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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364 cat("Checking XML structure...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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365 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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366 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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367 capture <- system(cmd, intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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368 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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369 if (length(capture)>0){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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372 write(capture, stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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374 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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375 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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376 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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377 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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378 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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379 # This function check if XML contain special characters |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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381 deleteXmlBadCharacters<- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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382 cat("Checking Non ASCII characters in the XML...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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383 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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384 processed <- F |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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385 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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386 for (i in l){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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388 capture <- suppressWarnings(system(cmd, intern=TRUE)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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389 if (length(capture)>0){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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392 c <- system(cmd, intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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393 capture <- "" |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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394 processed <- T |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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395 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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396 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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397 if (processed) cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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398 return(processed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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399 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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400 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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401 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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402 # This function will compute MD5 checksum to check the data integrity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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404 getMd5sum <- function (directory) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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405 cat("Compute md5 checksum...\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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406 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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407 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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409 info <- file.info(directory) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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411 files <- c(directory[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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412 exists <- file.exists(files) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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413 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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414 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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415 library(tools) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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416 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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417 #cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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418 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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419 return(as.matrix(md5sum(files))) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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420 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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421 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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422 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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423 # This function get the raw file path from the arguments |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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427 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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429 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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433 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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434 if (exists("singlefile_galaxyPaths")){ |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
437 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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438 singlefile <- NULL |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
442 # In case, an url is used to import data within Galaxy |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
445 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
446 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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447 return(list(zipfile=zipfile, singlefile=singlefile)) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
448 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
449 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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450 # This function retrieve the raw file in the working directory |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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451 # - if zipfile: unzip the file with its directory tree |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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452 # - if singlefiles: set symlink with the good filename |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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455 if(!is.null(singlefile) && (length("singlefile")>0)) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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456 for (singlefile_sampleName in names(singlefile)) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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458 if(!file.exists(singlefile_galaxyPath)){ |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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460 print(error_message); stop(error_message) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
461 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
462 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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464 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
465 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
466 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
467 directory <- "." |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
468 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
469 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
470 if(!is.null(zipfile) && (zipfile != "")) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
471 if(!file.exists(zipfile)){ |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
473 print(error_message) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
474 stop(error_message) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
475 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
476 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
477 #list all file in the zip file |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
478 #zip_files <- unzip(zipfile,list=T)[,"Name"] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
479 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
480 #unzip |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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481 suppressWarnings(unzip(zipfile, unzip="unzip")) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
482 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
483 #get the directory name |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
484 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
487 directory <- "." |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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488 if (length(directories) == 1) directory <- directories |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
489 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
490 cat("files_root_directory\t",directory,"\n") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
491 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
492 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
493 return (directory) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
494 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
495 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
496 |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
497 # This function retrieve a xset like object |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
499 getxcmsSetObject <- function(xobject) { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
500 # XCMS 1.x |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
501 if (class(xobject) == "xcmsSet") |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
502 return (xobject) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
503 # XCMS 3.x |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
504 if (class(xobject) == "XCMSnExp") { |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
505 # Get the legacy xcmsSet object |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
506 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
507 if (!is.null(xset@phenoData$sample_group)) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
508 sampclass(xset) <- xset@phenoData$sample_group |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
509 else |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
510 sampclass(xset) <- "." |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
511 return (xset) |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
512 } |
728ebc7ae7dd
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
513 } |