Mercurial > repos > lecorguille > camera_annotate
comparison CAMERA_annotateDiffreport.r @ 26:3d63a762954a draft default tip
planemo upload commit a923a432239a1f2ffee2dae1281fe2d8f41bac38
author | workflow4metabolomics |
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date | Mon, 30 Sep 2024 12:22:28 +0000 |
parents | 4b9ab71be05e |
children |
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25:4b9ab71be05e | 26:3d63a762954a |
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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") |