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annotate msnbase_readmsdata.r @ 14:cdebdb178031 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
author workflow4metabolomics
date Mon, 12 Apr 2021 09:34:31 +0000
parents cda005bc221c
children b25a582ab6c1
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1 #!/usr/bin/env Rscript
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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) {
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14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
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15 }
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16 source_local("lib.r")
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18 pkgs <- c("MSnbase", "batch")
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19 loadAndDisplayPackages(pkgs)
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20 cat("\n\n");
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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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31 # ----- PROCESSING INFILE -----
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32 cat("\tARGUMENTS PROCESSING INFO\n")
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35 cat("\n\n")
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37 # ----- INFILE PROCESSING -----
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38 cat("\tINFILE PROCESSING INFO\n")
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40 # Handle infiles
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41 if (!exists("singlefile")) singlefile <- NULL
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42 if (!exists("zipfile")) zipfile <- NULL
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43 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
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44 zipfile <- rawFilePath$zipfile
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45 singlefile <- rawFilePath$singlefile
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46 files <- rawFilePath$files
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48 md5sumList <- list("origin" = getMd5sum(files))
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50 cat("\n\n")
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53 # ----- MAIN PROCESSING INFO -----
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54 cat("\tMAIN PROCESSING INFO\n")
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57 cat("\t\tCOMPUTE\n")
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59 cat("\t\t\tCreate a phenodata data.frame\n")
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60 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x), "/")), n = 1))
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61 s_name <- tools::file_path_sans_ext(basename(files))
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62 pd <- data.frame(sample_name = s_name, sample_group = s_groups, stringsAsFactors = FALSE)
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63 print(pd)
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65 cat("\t\t\tLoad Raw Data\n")
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66 raw_data <- readMSData(files = files, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk")
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68 # Transform the files absolute pathways into relative pathways
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69 raw_data@processingData@files <- sub(paste(getwd(), "/", sep = ""), "", raw_data@processingData@files)
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71 # Create a sampleMetada file
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72 sampleNamesList <- getSampleMetadata(xdata = raw_data, sampleMetadataOutput = "sampleMetadata.tsv")
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74 cat("\n\n")
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76 # ----- EXPORT -----
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78 cat("\tMSnExp OBJECT INFO\n")
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79 print(raw_data)
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80 cat("\t\tphenoData\n")
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81 print(raw_data@phenoData@data)
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82 cat("\n\n")
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84 #saving R data in .Rdata file to save the variables used in the present tool
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85 objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
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86 save(list = objects2save[objects2save %in% ls()], file = "readmsdata.RData")
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89 cat("\tDONE\n")