Mercurial > repos > lecorguille > xcms_summary
annotate lib.r @ 17:4c37cd23e347 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author | lecorguille |
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date | Thu, 04 Oct 2018 10:38:43 -0400 |
parents | 97ca0321931b |
children | 0cc47a5ebca9 |
rev | line source |
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15
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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1 #@authors ABiMS TEAM, Y. Guitton |
97ca0321931b
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 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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3 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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4 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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5 # solve an issue with batch if arguments are logical TRUE/FALSE |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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6 parseCommandArgs <- function(...) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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7 args <- batch::parseCommandArgs(...) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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8 for (key in names(args)) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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9 if (args[key] %in% c("TRUE","FALSE")) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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10 args[key] = as.logical(args[key]) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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11 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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12 return(args) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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13 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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14 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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15 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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16 # This function will |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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17 # - load the packages |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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18 # - display the sessionInfo |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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19 loadAndDisplayPackages <- function(pkgs) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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21 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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22 sessioninfo = sessionInfo() |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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23 cat(sessioninfo$R.version$version.string,"\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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24 cat("Main packages:\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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26 cat("Other loaded packages:\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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28 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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29 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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30 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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31 # This function merge several chromBPI or chromTIC into one. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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32 mergeChrom <- function(chrom_merged, chrom) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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33 if (is.null(chrom_merged)) return(NULL) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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35 return(chrom_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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36 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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37 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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38 #@author G. Le Corguille |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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39 # This function merge several xdata into one. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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40 mergeXData <- function(args) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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changeset
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41 chromTIC <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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42 chromBPI <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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43 chromTIC_adjusted <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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44 chromBPI_adjusted <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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45 for(image in args$images) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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46 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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47 load(image) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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48 # Handle infiles |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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49 if (!exists("singlefile")) singlefile <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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50 if (!exists("zipfile")) zipfile <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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52 zipfile <- rawFilePath$zipfile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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53 singlefile <- rawFilePath$singlefile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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55 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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56 if (exists("raw_data")) xdata <- raw_data |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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58 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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59 cat(sampleNamesList$sampleNamesOrigin,"\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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60 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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61 if (!exists("xdata_merged")) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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62 xdata_merged <- xdata |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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63 singlefile_merged <- singlefile |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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64 md5sumList_merged <- md5sumList |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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65 sampleNamesList_merged <- sampleNamesList |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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66 chromTIC_merged <- chromTIC |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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67 chromBPI_merged <- chromBPI |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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68 chromTIC_adjusted_merged <- chromTIC_adjusted |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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69 chromBPI_adjusted_merged <- chromBPI_adjusted |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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70 } else { |
97ca0321931b
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) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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74 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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75 singlefile_merged <- c(singlefile_merged,singlefile) |
97ca0321931b
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$origin) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) |
97ca0321931b
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) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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83 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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84 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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85 rm(image) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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86 xdata <- xdata_merged; rm(xdata_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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87 singlefile <- singlefile_merged; rm(singlefile_merged) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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88 md5sumList <- md5sumList_merged; rm(md5sumList_merged) |
97ca0321931b
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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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91 if (!is.null(args$sampleMetadata)) { |
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92 cat("\tXSET PHENODATA SETTING...\n") |
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93 sampleMetadataFile <- args$sampleMetadata |
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94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) |
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95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] |
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96 |
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97 if (any(is.na(pData(xdata)$sample_group))) { |
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98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] |
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99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) |
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100 print(error_message) |
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101 stop(error_message) |
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102 } |
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103 } |
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104 |
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105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } |
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106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } |
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107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } |
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108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } |
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109 |
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110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) |
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111 } |
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112 |
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113 #@author G. Le Corguille |
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114 # This function convert if it is required the Retention Time in minutes |
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115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
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116 if (convertRTMinute){ |
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117 #converting the retention times (seconds) into minutes |
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118 print("converting the retention times into minutes in the variableMetadata") |
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119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 |
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120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 |
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121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 |
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122 } |
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123 return (variableMetadata) |
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124 } |
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125 |
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126 #@author G. Le Corguille |
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127 # This function format ions identifiers |
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128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { |
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129 splitDeco <- strsplit(as.character(variableMetadata$name),"_") |
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130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) |
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131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) |
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132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) |
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133 return(variableMetadata) |
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134 } |
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135 |
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136 #@author G. Le Corguille |
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137 # This function convert the remain NA to 0 in the dataMatrix |
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138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { |
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139 if (naTOzero){ |
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140 dataMatrix[is.na(dataMatrix)] <- 0 |
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141 } |
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142 return (dataMatrix) |
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143 } |
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144 |
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145 #@author G. Le Corguille |
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146 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) { |
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148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12) |
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149 |
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150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) |
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151 |
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152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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153 names(group_colors) <- unique(xdata$sample_group) |
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154 |
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155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) |
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156 for (i in 1:nrow(featureDefinitions(xdata))) { |
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157 mzmin = featureDefinitions(xdata)[i,]$mzmin |
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158 mzmax = featureDefinitions(xdata)[i,]$mzmax |
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159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) |
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160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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161 } |
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162 |
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163 dev.off() |
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164 } |
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165 |
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166 #@author G. Le Corguille |
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167 # Draw the plotChromPeakDensity 3 per page in a pdf file |
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168 getPlotAdjustedRtime <- function(xdata) { |
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169 |
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170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) |
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171 |
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172 # Color by group |
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173 group_colors <- brewer.pal(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=groupnamesW4M(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=groupnamesW4M(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 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) |
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202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) |
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203 |
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204 } |
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205 |
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206 #@author G. Le Corguille |
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207 # It allow different of field separators |
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208 getDataFrameFromFile <- function(filename, header=T) { |
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209 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) |
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210 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) |
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211 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) |
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212 if (ncol(myDataFrame) < 2) { |
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213 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" |
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214 print(error_message) |
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215 stop(error_message) |
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216 } |
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217 return(myDataFrame) |
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218 } |
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219 |
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220 #@author G. Le Corguille |
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221 # Draw the BPI and TIC graphics |
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222 # colored by sample names or class names |
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223 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { |
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224 |
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225 if (aggregationFun == "sum") |
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226 type="Total Ion Chromatograms" |
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227 else |
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228 type="Base Peak Intensity Chromatograms" |
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229 |
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230 adjusted="Raw" |
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231 if (hasAdjustedRtime(xdata)) |
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232 adjusted="Adjusted" |
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233 |
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234 main <- paste(type,":",adjusted,"data") |
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235 |
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236 pdf(pdfname, width=16, height=10) |
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237 |
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238 # Color by group |
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239 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] |
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240 if (length(group_colors) > 1) { |
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241 names(group_colors) <- unique(xdata$sample_group) |
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242 plot(chrom, col = group_colors[chrom$sample_group], main=main) |
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243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) |
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244 } |
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245 |
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246 # Color by sample |
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247 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main) |
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248 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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249 |
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250 dev.off() |
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251 } |
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252 |
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253 |
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254 # Get the polarities from all the samples of a condition |
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255 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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256 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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257 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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258 cat("Creating the sampleMetadata file...\n") |
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259 |
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260 #Create the sampleMetada dataframe |
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261 sampleMetadata <- xdata@phenoData@data |
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262 rownames(sampleMetadata) <- NULL |
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263 colnames(sampleMetadata) <- c("sampleMetadata", "class") |
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264 |
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265 sampleNamesOrigin <- sampleMetadata$sampleMetadata |
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266 sampleNamesMakeNames <- make.names(sampleNamesOrigin) |
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267 |
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268 if (any(duplicated(sampleNamesMakeNames))) { |
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269 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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270 for (sampleName in sampleNamesOrigin) { |
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271 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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272 } |
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273 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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274 } |
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275 |
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276 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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277 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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278 for (sampleName in sampleNamesOrigin) { |
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279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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280 } |
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281 } |
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282 |
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283 sampleMetadata$sampleMetadata <- sampleNamesMakeNames |
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284 |
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285 |
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286 #For each sample file, the following actions are done |
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287 for (fileIdx in 1:length(fileNames(xdata))) { |
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288 #Check if the file is in the CDF format |
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289 if (!mzR:::netCDFIsFile(fileNames(xdata))) { |
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290 |
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291 # If the column isn't exist, with add one filled with NA |
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292 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA |
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293 |
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294 #Extract the polarity (a list of polarities) |
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295 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] |
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296 #Verify if all the scans have the same polarity |
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297 uniq_list <- unique(polarity) |
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298 if (length(uniq_list)>1){ |
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299 polarity <- "mixed" |
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300 } else { |
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301 polarity <- as.character(uniq_list) |
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302 } |
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303 |
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304 #Set the polarity attribute |
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305 sampleMetadata$polarity[fileIdx] <- polarity |
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306 } |
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307 |
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308 } |
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309 |
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310 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
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311 |
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312 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) |
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313 |
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314 } |
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315 |
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316 |
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317 # This function check if xcms will found all the files |
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318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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319 checkFilesCompatibilityWithXcms <- function(directory) { |
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320 cat("Checking files filenames compatibilities with xmcs...\n") |
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321 # WHAT XCMS WILL FIND |
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322 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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323 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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324 info <- file.info(directory) |
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325 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
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326 files <- c(directory[!info$isdir], listed) |
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327 files_abs <- file.path(getwd(), files) |
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328 exists <- file.exists(files_abs) |
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329 files[exists] <- files_abs[exists] |
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330 files[exists] <- sub("//","/",files[exists]) |
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331 |
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332 # WHAT IS ON THE FILESYSTEM |
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333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) |
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334 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
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335 |
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336 # COMPARISON |
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337 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
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338 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
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339 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
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340 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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341 } |
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342 } |
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343 |
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344 |
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345 #This function list the compatible files within the directory as xcms did |
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346 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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347 getMSFiles <- function (directory) { |
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348 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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349 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
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350 info <- file.info(directory) |
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351 listed <- list.files(directory[info$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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352 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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353 exists <- file.exists(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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354 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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355 return(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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356 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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357 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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358 # This function check if XML contains special caracters. It also checks integrity and completness. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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360 checkXmlStructure <- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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361 cat("Checking XML structure...\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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362 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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363 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;") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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364 capture <- system(cmd, intern=TRUE) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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365 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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366 if (length(capture)>0){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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367 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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368 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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369 write(capture, stderr()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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370 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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371 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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372 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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373 } |
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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 # This function check if XML contain special characters |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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377 #@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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378 deleteXmlBadCharacters<- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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379 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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380 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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381 processed <- F |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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382 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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383 for (i in l){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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385 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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386 if (length(capture)>0){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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389 c <- system(cmd, intern=TRUE) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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390 capture <- "" |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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391 processed <- T |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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392 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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393 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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394 if (processed) cat("\n\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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395 return(processed) |
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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 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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398 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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399 # This function will compute MD5 checksum to check the data integrity |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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401 getMd5sum <- function (directory) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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402 cat("Compute md5 checksum...\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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403 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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404 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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405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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406 info <- file.info(directory) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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408 files <- c(directory[!info$isdir], listed) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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409 exists <- file.exists(files) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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410 files <- files[exists] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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411 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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412 library(tools) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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413 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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414 #cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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415 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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416 return(as.matrix(md5sum(files))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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417 } |
97ca0321931b
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 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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420 # This function get the raw file path from the arguments |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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424 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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426 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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|
429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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parents:
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430 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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|
431 if (exists("singlefile_galaxyPaths")){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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434 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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|
435 singlefile <- NULL |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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parents:
diff
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436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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|
437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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|
439 # In case, an url is used to import data within Galaxy |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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parents:
diff
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440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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442 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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443 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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444 return(list(zipfile=zipfile, singlefile=singlefile)) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
445 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
446 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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447 # This function retrieve the raw file in the working directory |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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448 # - if zipfile: unzip the file with its directory tree |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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449 # - if singlefiles: set symlink with the good filename |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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452 if(!is.null(singlefile) && (length("singlefile")>0)) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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453 for (singlefile_sampleName in names(singlefile)) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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455 if(!file.exists(singlefile_galaxyPath)){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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456 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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457 print(error_message); stop(error_message) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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458 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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459 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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461 file.copy(singlefile_galaxyPath, singlefile_sampleName) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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462 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
463 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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464 directory <- "." |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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465 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
466 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
467 if(!is.null(zipfile) && (zipfile != "")) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
468 if(!file.exists(zipfile)){ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
470 print(error_message) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
471 stop(error_message) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
472 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
473 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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474 #list all file in the zip file |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
475 #zip_files <- unzip(zipfile,list=T)[,"Name"] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
476 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
477 #unzip |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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478 suppressWarnings(unzip(zipfile, unzip="unzip")) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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479 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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480 #get the directory name |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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481 suppressWarnings(filesInZip <- unzip(zipfile, list=T)) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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484 directory <- "." |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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485 if (length(directories) == 1) directory <- directories |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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486 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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487 cat("files_root_directory\t",directory,"\n") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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parents:
diff
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488 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
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489 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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490 return (directory) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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491 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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492 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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diff
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493 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
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494 # This function retrieve a xset like object |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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|
495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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496 getxcmsSetObject <- function(xobject) { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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497 # XCMS 1.x |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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498 if (class(xobject) == "xcmsSet") |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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499 return (xobject) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
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|
500 # XCMS 3.x |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
501 if (class(xobject) == "XCMSnExp") { |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
502 # Get the legacy xcmsSet object |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
503 suppressWarnings(xset <- as(xobject, 'xcmsSet')) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
504 if (!is.null(xset@phenoData$sample_group)) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
505 sampclass(xset) <- xset@phenoData$sample_group |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
506 else |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
507 sampclass(xset) <- "." |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
508 return (xset) |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
509 } |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents:
diff
changeset
|
510 } |