Mercurial > repos > lecorguille > camera_annotate

comparison CAMERA_annotateDiffreport.r @ 18:cb923396e70f draft

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planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
author lecorguille
date Thu, 29 Aug 2019 11:38:21 -0400
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children 01459b73daf9
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17:73d82de36369 18:cb923396e70f
1 #!/usr/bin/env Rscript
2
3 # ----- PACKAGE -----
4 cat("\tSESSION INFO\n")
5
6 #Import the different functions
7 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
8 source_local("lib.r")
9
10 pkgs=c("CAMERA","multtest","batch")
11 loadAndDisplayPackages(pkgs)
12 cat("\n\n");
13
14 # ----- ARGUMENTS -----
15 cat("\tARGUMENTS INFO\n")
16
17 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
18 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
19
20 cat("\n\n");
21
22
23 # ----- PROCESSING INFILE -----
24 cat("\tINFILE PROCESSING INFO\n")
25
26 #image is an .RData file necessary to use xset variable given by previous tools
27 load(args$image); args$image=NULL
28
29 cat("\n\n")
30
31
32 # ----- ARGUMENTS PROCESSING -----
33 cat("\tARGUMENTS PROCESSING INFO\n")
34
35 # Save arguments to generate a report
36 if (!exists("listOFargs")) listOFargs=list()
37 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args
38
39 # We unzip automatically the chromatograms from the zip files.
40 if (!exists("zipfile")) zipfile=NULL
41 if (!exists("singlefile")) singlefile=NULL
42 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
43 zipfile = rawFilePath$zipfile
44 singlefile = rawFilePath$singlefile
45 args = rawFilePath$args
46 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
47
48 # Because so far CAMERA isn't compatible with the new XCMSnExp object
49 if (exists("xdata")){
50 xset <- getxcmsSetObject(xdata)
51 }
52
53 cat("\n\n")
54
55
56 # ----- PROCESSING INFO -----
57 cat("\tMAIN PROCESSING INFO\n")
58
59 results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
60 xa=results_list$xa
61 diffrep=results_list$diffrep
62 variableMetadata=results_list$variableMetadata
63
64 cat("\n\n")
65
66 # ----- EXPORT -----
67
68 cat("\tXSET OBJECT INFO\n")
69 print(xa)
70 cat("\n\n")
71
72 #saving R data in .Rdata file to save the variables used in the present tool
73 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
74 save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData")
75
76 cat("\n\n")
77
78 cat("\tDONE\n")