Mercurial > repos > lecorguille > camera_annotate

comparison CAMERA_annotateDiffreport.r @ 26:3d63a762954a draft default tip

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planemo upload commit a923a432239a1f2ffee2dae1281fe2d8f41bac38
author workflow4metabolomics
date Mon, 30 Sep 2024 12:22:28 +0000
parents 4b9ab71be05e
children
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25:4b9ab71be05e 26:3d63a762954a
33 33
34 # ----- ARGUMENTS PROCESSING ----- 34 # ----- ARGUMENTS PROCESSING -----
35 cat("\tARGUMENTS PROCESSING INFO\n") 35 cat("\tARGUMENTS PROCESSING INFO\n")
36 36
37 # Save arguments to generate a report 37 # Save arguments to generate a report
38 if (!exists("listOFargs")) listOFargs <- list() 38 if (!exists("listOFlistArguments")) listOFlistArguments <- list()
39 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] <- args 39 listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] <- args
40 40
41 # We unzip automatically the chromatograms from the zip files. 41 # We unzip automatically the chromatograms from the zip files.
42 if (!exists("zipfile")) zipfile <- NULL 42 if (!exists("zipfile")) zipfile <- NULL
43 if (!exists("singlefile")) singlefile <- NULL 43 if (!exists("singlefile")) singlefile <- NULL
44 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) 44 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
71 cat("\tXSET OBJECT INFO\n") 71 cat("\tXSET OBJECT INFO\n")
72 print(xa) 72 print(xa)
73 cat("\n\n") 73 cat("\n\n")
74 74
75 # saving R data in .Rdata file to save the variables used in the present tool 75 # saving R data in .Rdata file to save the variables used in the present tool
76 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile") 76 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFlistArguments", "zipfile", "singlefile")
77 save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData") 77 save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData")
78 78
79 cat("\n\n") 79 cat("\n\n")
80 80
81 cat("\tDONE\n") 81 cat("\tDONE\n")