Mercurial > repos > lecorguille > xcms_retcor
annotate xcms_retcor.r @ 27:8242376d9f35 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
author | workflow4metabolomics |
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date | Thu, 14 Mar 2024 15:35:44 +0000 |
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rev | line source |
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27
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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1 #!/usr/bin/env Rscript |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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2 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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3 # ----- LOG FILE ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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4 log_file <- file("log.txt", open = "wt") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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5 sink(log_file) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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6 sink(log_file, type = "output") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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7 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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9 # ----- PACKAGE ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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10 cat("\tSESSION INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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11 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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12 #Import the different functions |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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13 source_local <- function(fname) { |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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14 argv <- commandArgs(trailingOnly = FALSE) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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16 source(paste(base_dir, fname, sep = "/")) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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17 } |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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18 source_local("lib.r") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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19 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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20 pkgs <- c("xcms", "batch", "RColorBrewer") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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21 loadAndDisplayPackages(pkgs) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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22 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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23 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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24 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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25 # ----- ARGUMENTS ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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26 cat("\tARGUMENTS INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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27 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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29 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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30 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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31 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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32 # ----- PROCESSING INFILE ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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33 cat("\tARGUMENTS PROCESSING INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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34 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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35 #saving the specific parameters |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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36 method <- args$method |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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37 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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38 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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39 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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40 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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41 # ----- ARGUMENTS PROCESSING ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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42 cat("\tINFILE PROCESSING INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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43 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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44 #image is an .RData file necessary to use xset variable given by previous tools |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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45 load(args$image) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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46 args$image <- NULL |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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47 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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48 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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49 # Handle infiles |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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50 if (!exists("singlefile")) singlefile <- NULL |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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51 if (!exists("zipfile")) zipfile <- NULL |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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52 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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53 zipfile <- rawFilePath$zipfile |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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54 singlefile <- rawFilePath$singlefile |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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55 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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56 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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57 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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58 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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59 # ----- MAIN PROCESSING INFO ----- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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60 cat("\tMAIN PROCESSING INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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61 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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62 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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63 cat("\t\tCOMPUTE\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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64 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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65 cat("\t\t\tAlignment/Retention Time correction\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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66 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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67 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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68 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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69 adjustRtimeParam <- do.call(paste0(method, "Param"), args) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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70 print(adjustRtimeParam) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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71 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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72 if (hasAdjustedRtime(xdata)) { |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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73 cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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74 cat("Replace raw retention times with adjusted retention times.\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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75 xdata <- applyAdjustedRtime(xdata) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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76 } |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
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77 xdata <- adjustRtime(xdata, param = adjustRtimeParam) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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78 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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79 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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80 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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81 |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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82 # -- TIC -- |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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83 cat("\t\tDRAW GRAPHICS\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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84 getPlotAdjustedRtime(xdata) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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85 |
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86 cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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87 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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88 # ----- EXPORT ----- |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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89 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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90 cat("\tXCMSnExp OBJECT INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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91 print(xdata) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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92 cat("\n\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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93 |
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94 cat("\txcmsSet OBJECT INFO\n") |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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95 # Get the legacy xcmsSet object |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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96 xset <- getxcmsSetObject(xdata) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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97 print(xset) |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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98 cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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99 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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100 #saving R data in .Rdata file to save the variables used in the present tool |
8242376d9f35
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
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101 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") |
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102 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData") |
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103 |
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104 cat("\n\n") |
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105 |
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106 |
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107 cat("\tDONE\n") |