Mercurial > repos > lecorguille > xcms_retcor

annotate xcms_retcor.r @ 50:0bc08f128b42 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:41:19 +0000
parents 177b5847a211
children
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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1 #!/usr/bin/env Rscript
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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3 # ----- LOG FILE -----
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4 log_file <- file("log.txt", open = "wt")
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5 sink(log_file)
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6 sink(log_file, type = "output")
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 # Import the different functions
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13 source_local <- function(fname) {
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14 argv <- commandArgs(trailingOnly = FALSE)
0bc08f128b42 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
0bc08f128b42 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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16 source(paste(base_dir, fname, sep = "/"))
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17 }
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18 source_local("lib.r")
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20 pkgs <- c("xcms", "batch", "RColorBrewer")
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21 loadAndDisplayPackages(pkgs)
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22 cat("\n\n")
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25 # ----- ARGUMENTS -----
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26 cat("\tARGUMENTS INFO\n")
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27 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
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28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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30 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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32 # ----- PROCESSING INFILE -----
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33 cat("\tARGUMENTS PROCESSING INFO\n")
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35 # saving the specific parameters
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36 method <- args$method
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38 cat("\n\n")
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41 # ----- ARGUMENTS PROCESSING -----
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42 cat("\tINFILE PROCESSING INFO\n")
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44 # image is an .RData file necessary to use xset variable given by previous tools
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45 load(args$image)
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46 args$image <- NULL
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47 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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49 # Handle infiles
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50 if (!exists("singlefile")) singlefile <- NULL
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51 if (!exists("zipfile")) zipfile <- NULL
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52 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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53 zipfile <- rawFilePath$zipfile
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54 singlefile <- rawFilePath$singlefile
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56 cat("\n\n")
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59 # ----- MAIN PROCESSING INFO -----
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60 cat("\tMAIN PROCESSING INFO\n")
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63 cat("\t\tCOMPUTE\n")
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65 cat("\t\t\tAlignment/Retention Time correction\n")
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66 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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67 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
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68
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69 adjustRtimeParam <- do.call(paste0(method, "Param"), args)
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70 print(adjustRtimeParam)
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72 if (hasAdjustedRtime(xdata)) {
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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")
0bc08f128b42 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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74 cat("Replace raw retention times with adjusted retention times.\n")
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75 xdata <- applyAdjustedRtime(xdata)
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76 }
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77 xdata <- adjustRtime(xdata, param = adjustRtimeParam)
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78
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79 cat("\n\n")
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82 # -- TIC --
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83 cat("\t\tDRAW GRAPHICS\n")
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84 getPlotAdjustedRtime(xdata)
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86 cat("\n\n")
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88 # ----- EXPORT -----
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90 cat("\tXCMSnExp OBJECT INFO\n")
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91 print(xdata)
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92 cat("\n\n")
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93
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94 cat("\txcmsSet OBJECT INFO\n")
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95 # Get the legacy xcmsSet object
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96 xset <- getxcmsSetObject(xdata)
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97 print(xset)
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98 cat("\n\n")
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99
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0bc08f128b42 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
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100 # saving R data in .Rdata file to save the variables used in the present tool
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366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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101 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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102 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")
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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")