Mercurial > repos > lecorguille > xcms_retcor

annotate xcms_retcor.r @ 48:366ff564f949 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 10:31:56 +0000
parents 32c1cbdbdd3b
children 177b5847a211
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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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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) {
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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15 }
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16 source_local("lib.r")
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18 pkgs <- c("xcms", "batch", "RColorBrewer")
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19 loadAndDisplayPackages(pkgs)
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20 cat("\n\n");
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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23 # ----- ARGUMENTS -----
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24 cat("\tARGUMENTS INFO\n")
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25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
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28 cat("\n\n")
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30 # ----- PROCESSING INFILE -----
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31 cat("\tARGUMENTS PROCESSING INFO\n")
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33 #saving the specific parameters
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34 method <- args$method
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36 cat("\n\n")
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39 # ----- ARGUMENTS PROCESSING -----
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40 cat("\tINFILE PROCESSING INFO\n")
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42 #image is an .RData file necessary to use xset variable given by previous tools
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43 load(args$image); args$image <- NULL
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44 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
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46 # Handle infiles
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47 if (!exists("singlefile")) singlefile <- NULL
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48 if (!exists("zipfile")) zipfile <- NULL
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49 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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50 zipfile <- rawFilePath$zipfile
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51 singlefile <- rawFilePath$singlefile
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53 cat("\n\n")
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56 # ----- MAIN PROCESSING INFO -----
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57 cat("\tMAIN PROCESSING INFO\n")
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60 cat("\t\tCOMPUTE\n")
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62 cat("\t\t\tAlignment/Retention Time correction\n")
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63 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
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64 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
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65
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66 adjustRtimeParam <- do.call(paste0(method, "Param"), args)
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67 print(adjustRtimeParam)
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69 if (hasAdjustedRtime(xdata)) {
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70 cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
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71 cat("Replace raw retention times with adjusted retention times.\n")
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72 xdata <- applyAdjustedRtime(xdata)
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73 }
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74 xdata <- adjustRtime(xdata, param = adjustRtimeParam)
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75
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76 cat("\n\n")
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79 # -- TIC --
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80 cat("\t\tDRAW GRAPHICS\n")
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81 getPlotAdjustedRtime(xdata)
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83 cat("\n\n")
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85 # ----- EXPORT -----
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87 cat("\tXCMSnExp OBJECT INFO\n")
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88 print(xdata)
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89 cat("\n\n")
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91 cat("\txcmsSet OBJECT INFO\n")
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92 # Get the legacy xcmsSet object
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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93 xset <- getxcmsSetObject(xdata)
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4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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94 print(xset)
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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95 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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96
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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97 #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"
workflow4metabolomics
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98 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
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99 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")
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100
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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101 cat("\n\n")
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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102
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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103
4d6f4cd7c3ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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104 cat("\tDONE\n")