Mercurial > repos > workflow4metabolomics > camera_combinexsannos
annotate CAMERA_combinexsAnnos.r @ 4:4c4945bce185 draft
"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
author | workflow4metabolomics |
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date | Thu, 22 Apr 2021 10:27:58 +0000 |
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children | 2443150161b4 |
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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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5 |
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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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11 |
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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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15 |
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16 # ----- ARGUMENTS ----- |
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17 cat("\tARGUMENTS INFO\n") |
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18 |
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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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21 |
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22 cat("\n\n"); |
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23 |
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24 |
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25 # ----- PROCESSING INFILE ----- |
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26 cat("\tINFILE PROCESSING INFO\n") |
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27 |
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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$image_pos) |
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30 xaP <- xa |
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31 |
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32 diffrepP <- NULL |
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33 if (exists("diffrep")) diffrepP <- diffrep |
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34 |
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35 load(args$image_neg) |
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36 xaN <- xa |
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37 |
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38 diffrepN <- NULL |
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39 if (exists("diffrep")) diffrepN <- diffrep |
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40 |
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41 |
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42 cat("\n\n") |
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44 |
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45 # ----- ARGUMENTS PROCESSING ----- |
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46 cat("\tARGUMENTS PROCESSING INFO\n") |
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47 |
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48 # Save arguments to generate a report |
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49 if (!exists("listOFargs")) listOFargs <- list() |
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50 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] <- args |
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51 |
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52 cat("\n\n") |
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53 |
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54 |
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55 # ----- PROCESSING INFO ----- |
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56 cat("\tMAIN PROCESSING INFO\n") |
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57 |
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58 cAnnot <- combinexsAnnos_function( |
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59 xaP = xaP, xaN = xaN, |
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60 diffrepP = diffrepP, diffrepN = diffrepN, |
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61 pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta, |
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62 convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT, |
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63 variableMetadataOutput = "variableMetadata.tsv" |
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64 ) |
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65 |
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66 # ----- EXPORT ----- |
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67 |
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68 #saving R data in .Rdata file to save the variables used in the present tool |
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69 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile") |
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70 save(list = objects2save[objects2save %in% ls()], file = "combinexsAnnos.RData") |
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71 |
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72 cat("\n\n") |
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73 |
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74 cat("\tDONE\n") |