Mercurial > repos > lecorguille > camera_annotate

annotate CAMERA_annotateDiffreport.r @ 24:512c2b701d96 draft

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"planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
author workflow4metabolomics
date Fri, 02 Jul 2021 02:51:41 +0000
parents abf1775ac14d
children 4b9ab71be05e
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1 #!/usr/bin/env Rscript
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2
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3 # ----- PACKAGE -----
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4 cat("\tSESSION INFO\n")
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6 #Import the different functions
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7 source_local <- function(fname) {
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8 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
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9 }
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10 source_local("lib.r")
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12 pkgs <- c("CAMERA", "multtest", "batch")
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13 loadAndDisplayPackages(pkgs)
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14 cat("\n\n");
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16 # ----- ARGUMENTS -----
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17 cat("\tARGUMENTS INFO\n")
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19 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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20 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
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22 cat("\n\n");
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25 # ----- PROCESSING INFILE -----
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26 cat("\tINFILE PROCESSING INFO\n")
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28 #image is an .RData file necessary to use xset variable given by previous tools
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29 load(args$image); args$image <- NULL
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31 cat("\n\n")
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34 # ----- ARGUMENTS PROCESSING -----
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35 cat("\tARGUMENTS PROCESSING INFO\n")
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37 # Save arguments to generate a report
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38 if (!exists("listOFargs")) listOFargs <- list()
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39 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] <- args
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41 # We unzip automatically the chromatograms from the zip files.
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42 if (!exists("zipfile")) zipfile <- NULL
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43 if (!exists("singlefile")) singlefile <- NULL
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44 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
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45 zipfile <- rawFilePath$zipfile
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46 singlefile <- rawFilePath$singlefile
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47 args <- rawFilePath$args
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48 directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
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51 # Because so far CAMERA isn't compatible with the new XCMSnExp object
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52 if (exists("xdata")) {
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53 xset <- getxcmsSetObject(xdata)
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54 }
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56 cat("\n\n")
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59 # ----- PROCESSING INFO -----
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60 cat("\tMAIN PROCESSING INFO\n")
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62 results_list <- annotatediff(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv")
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63 xa <- results_list$xa
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64 diffrep <- results_list$diffrep
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65 variableMetadata <- results_list$variableMetadata
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67 cat("\n\n")
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69 # ----- EXPORT -----
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70
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71 cat("\tXSET OBJECT INFO\n")
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72 print(xa)
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73 cat("\n\n")
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75 #saving R data in .Rdata file to save the variables used in the present tool
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76 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile")
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77 save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData")
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79 cat("\n\n")
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81 cat("\tDONE\n")