Mercurial > repos > workflow4metabolomics > camera_combinexsannos

comparison CAMERA_combinexsAnnos.r @ 4:4c4945bce185 draft

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"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
author workflow4metabolomics
date Thu, 22 Apr 2021 10:27:58 +0000
parents 139ff66b0b5d
children 2443150161b4
comparison
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3:3bf04fc404d9 4:4c4945bce185
2 2
3 # ----- PACKAGE ----- 3 # ----- PACKAGE -----
4 cat("\tSESSION INFO\n") 4 cat("\tSESSION INFO\n")
5 5
6 #Import the different functions 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="/")) } 7 source_local <- function(fname) {
8 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
9 }
8 source_local("lib.r") 10 source_local("lib.r")
9 11
10 pkgs=c("CAMERA","multtest","batch") 12 pkgs <- c("CAMERA", "multtest", "batch")
11 loadAndDisplayPackages(pkgs) 13 loadAndDisplayPackages(pkgs)
12 cat("\n\n"); 14 cat("\n\n");
13 15
14 # ----- ARGUMENTS ----- 16 # ----- ARGUMENTS -----
15 cat("\tARGUMENTS INFO\n") 17 cat("\tARGUMENTS INFO\n")
16 18
17 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects 19 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') 20 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
19 21
20 cat("\n\n"); 22 cat("\n\n");
21 23
22 24
23 # ----- PROCESSING INFILE ----- 25 # ----- PROCESSING INFILE -----
24 cat("\tINFILE PROCESSING INFO\n") 26 cat("\tINFILE PROCESSING INFO\n")
25 27
26 #image is an .RData file necessary to use xset variable given by previous tools 28 #image is an .RData file necessary to use xset variable given by previous tools
27 load(args$image_pos) 29 load(args$image_pos)
28 xaP=xa 30 xaP <- xa
29 31
30 diffrepP=NULL 32 diffrepP <- NULL
31 if (exists("diffrep")) diffrepP=diffrep 33 if (exists("diffrep")) diffrepP <- diffrep
32 34
33 load(args$image_neg) 35 load(args$image_neg)
34 xaN=xa 36 xaN <- xa
35 37
36 diffrepN=NULL 38 diffrepN <- NULL
37 if (exists("diffrep")) diffrepN=diffrep 39 if (exists("diffrep")) diffrepN <- diffrep
38 40
39 41
40 cat("\n\n") 42 cat("\n\n")
41 43
42 44
43 # ----- ARGUMENTS PROCESSING ----- 45 # ----- ARGUMENTS PROCESSING -----
44 cat("\tARGUMENTS PROCESSING INFO\n") 46 cat("\tARGUMENTS PROCESSING INFO\n")
45 47
46 # Save arguments to generate a report 48 # Save arguments to generate a report
47 if (!exists("listOFargs")) listOFargs=list() 49 if (!exists("listOFargs")) listOFargs <- list()
48 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] = args 50 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_combinexsAnnos")]] <- args
49 51
50 cat("\n\n") 52 cat("\n\n")
51 53
52 54
53 # ----- PROCESSING INFO ----- 55 # ----- PROCESSING INFO -----
54 cat("\tMAIN PROCESSING INFO\n") 56 cat("\tMAIN PROCESSING INFO\n")
55 57
56 cAnnot=combinexsAnnos_function( 58 cAnnot <- combinexsAnnos_function(
57 xaP=xaP,xaN=xaN, 59 xaP = xaP, xaN = xaN,
58 diffrepP=diffrepP, diffrepN=diffrepN, 60 diffrepP = diffrepP, diffrepN = diffrepN,
59 pos=args$pos, tol=args$tol,ruleset=args$ruleset, keep_meta=args$keep_meta, 61 pos = args$pos, tol = args$tol, ruleset = args$ruleset, keep_meta = args$keep_meta,
60 convertRTMinute=args$convertRTMinute, numDigitsMZ=args$numDigitsMZ, numDigitsRT=args$numDigitsRT, 62 convertRTMinute = args$convertRTMinute, numDigitsMZ = args$numDigitsMZ, numDigitsRT = args$numDigitsRT,
61 variableMetadataOutput="variableMetadata.tsv" 63 variableMetadataOutput = "variableMetadata.tsv"
62 ) 64 )
63 65
64 # ----- EXPORT ----- 66 # ----- EXPORT -----
65 67
66 #saving R data in .Rdata file to save the variables used in the present tool 68 #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") 69 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile")
68 save(list=objects2save[objects2save %in% ls()], file="combinexsAnnos.RData") 70 save(list = objects2save[objects2save %in% ls()], file = "combinexsAnnos.RData")
69 71
70 cat("\n\n") 72 cat("\n\n")
71 73
72 cat("\tDONE\n") 74 cat("\tDONE\n")