Mercurial > repos > workflow4metabolomics > camera_combinexsannos

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planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
author workflow4metabolomics
date Mon, 11 Sep 2023 22:41:22 +0000
parents 4c4945bce185
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1 #!/usr/bin/env Rscript
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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)
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9 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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10 source(paste(base_dir, fname, sep = "/"))
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11 }
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12 source_local("lib.r")
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14 pkgs <- c("CAMERA", "multtest", "batch")
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15 loadAndDisplayPackages(pkgs)
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16 cat("\n\n")
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18 # ----- ARGUMENTS -----
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19 cat("\tARGUMENTS INFO\n")
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21 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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22 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
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24 cat("\n\n")
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27 # ----- PROCESSING INFILE -----
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28 cat("\tINFILE PROCESSING INFO\n")
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30 #image is an .RData file necessary to use xset variable given by previous tools
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31 load(args$image_pos)
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32 xaP <- xa
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34 diffrepP <- NULL
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35 if (exists("diffrep")) diffrepP <- diffrep
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37 load(args$image_neg)
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38 xaN <- xa
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40 diffrepN <- NULL
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41 if (exists("diffrep")) diffrepN <- diffrep
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44 cat("\n\n")
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47 # ----- ARGUMENTS PROCESSING -----
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48 cat("\tARGUMENTS PROCESSING INFO\n")
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50 # Save arguments to generate a report
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51 if (!exists("listOFargs")) listOFargs <- list()
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52 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] <- args
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54 cat("\n\n")
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57 # ----- PROCESSING INFO -----
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58 cat("\tMAIN PROCESSING INFO\n")
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60 cAnnot <- combinexsAnnos_function(
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61 xaP = xaP, xaN = xaN,
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62 diffrepP = diffrepP, diffrepN = diffrepN,
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63 pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta,
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64 convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT,
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65 variableMetadataOutput = "variableMetadata.tsv"
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66 )
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68 # ----- EXPORT -----
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70 #saving R data in .Rdata file to save the variables used in the present tool
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71 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile")
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72 save(list = objects2save[objects2save %in% ls()], file = "combinexsAnnos.RData")
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74 cat("\n\n")
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76 cat("\tDONE\n")