Mercurial > repos > workflow4metabolomics > camera_combinexsannos
comparison CAMERA_combinexsAnnos.r @ 0:139ff66b0b5d draft
planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464
author | workflow4metabolomics |
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date | Fri, 26 Jul 2019 16:49:18 -0400 |
parents | |
children | 4c4945bce185 |
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-1:000000000000 | 0:139ff66b0b5d |
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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$image_pos) | |
28 xaP=xa | |
29 | |
30 diffrepP=NULL | |
31 if (exists("diffrep")) diffrepP=diffrep | |
32 | |
33 load(args$image_neg) | |
34 xaN=xa | |
35 | |
36 diffrepN=NULL | |
37 if (exists("diffrep")) diffrepN=diffrep | |
38 | |
39 | |
40 cat("\n\n") | |
41 | |
42 | |
43 # ----- ARGUMENTS PROCESSING ----- | |
44 cat("\tARGUMENTS PROCESSING INFO\n") | |
45 | |
46 # Save arguments to generate a report | |
47 if (!exists("listOFargs")) listOFargs=list() | |
48 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args | |
49 | |
50 cat("\n\n") | |
51 | |
52 | |
53 # ----- PROCESSING INFO ----- | |
54 cat("\tMAIN PROCESSING INFO\n") | |
55 | |
56 cAnnot=combinexsAnnos_function( | |
57 xaP=xaP,xaN=xaN, | |
58 diffrepP=diffrepP, diffrepN=diffrepN, | |
59 pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta, | |
60 convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT, | |
61 variableMetadataOutput="variableMetadata.tsv" | |
62 ) | |
63 | |
64 # ----- EXPORT ----- | |
65 | |
66 #saving R data in .Rdata file to save the variables used in the present tool | |
67 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile") | |
68 save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData") | |
69 | |
70 cat("\n\n") | |
71 | |
72 cat("\tDONE\n") |