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comparison probmetab.r @ 0:e13ec2c3fabe draft

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planemo upload commit 25fd6a739741295e3f434e0be0286dee61e06825
author mmonsoor
date Mon, 04 Jul 2016 04:29:25 -0400
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children abcfa1648b66
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-1:000000000000 0:e13ec2c3fabe
1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
2 # probmetab.r version="1.0.0"
3 # Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
4
5
6 # ----- LOG -----
7 log_file=file("probmetab.log", open = "wt")
8 sink(log_file)
9 sink(log_file, type = "out")
10
11 # ----- PACKAGE -----
12 cat("\tPACKAGE INFO\n")
13 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
14 for(p in pkgs) {
15 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
16 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
17 }
18
19 source_local <- function(fname){
20 argv <- commandArgs(trailingOnly = FALSE)
21 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
22 source(paste(base_dir, fname, sep="/"))
23 }
24 cat("\n\n")
25 # ----- ARGUMENTS -----
26 cat("\tARGUMENTS INFO\n")
27 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
28 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
29
30
31
32 # ----- PROCESSING INFILE -----
33 cat("\tINFILE PROCESSING INFO\n")
34
35 # ----- INFILE PROCESSING -----
36
37 if(listArguments[["mode_acquisition"]]=="one") {
38 load(listArguments[["xa"]])
39
40 if (!is.null(listArguments[["zipfile"]])){
41 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
42 }
43
44 #Unzip the chromatograms file for plotting EIC pour the HTML file
45 if(exists("zipfile"))
46 {
47 if (zipfile!=""){
48 directory=unzip(zipfile)
49 }
50 }
51 if (!exists("xa")) {
52 xa=xsAnnotate_object
53 }
54 source_local("lib.r")
55 if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
56
57 } else if(listArguments[["inputs_mode"]]=="two"){
58 load(listArguments[["image_pos"]])
59
60 if (!is.null(listArguments[["zipfile"]])){
61 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
62 }
63
64 #Unzip the chromatograms file for plotting EIC pour the HTML file
65 if(exists("zipfile")) {
66 if (zipfile!=""){
67 directory=unzip(zipfile)
68 }
69 }
70 if (!exists("xa")) {
71 xa=xsAnnotate_object
72 }
73 xaP=xa
74 source_local("lib.r")
75 if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa)
76 else variableMetadataP=variableMetadata
77
78
79 load(listArguments[["image_neg"]])
80
81 if (!is.null(listArguments[["zipfile"]])){
82 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
83 }
84
85 #Unzip the chromatograms file for plotting EIC pour the HTML file
86 if(exists("zipfile")) {
87
88 if (zipfile!=""){
89 directory=unzip(zipfile)
90 }
91 }
92 if (!exists("xa")) {
93 xa=xsAnnotate_object
94 }
95 xaN=xa
96 source_local("lib.r")
97
98 if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa)
99 else variableMetadataN=variableMetadata
100 }
101
102 #Import the different functions
103 source_local("lib.r")
104 source_local("export.class.table-color-graph.R")
105
106 # ----- PROCESSING INFO -----
107 cat("\tMAIN PROCESSING INFO\n")
108
109 if(listArguments[["mode_acquisition"]]=="one") {
110 results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
111 } else if(listArguments[["inputs_mode"]]=="two"){
112 results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
113 }
114 #delete the parameters to avoid the passage to the next tool in .RData image
115 #rm(listArguments)
116 cat("\tDONE\n")
117 #saving R data in .Rdata file to save the variables used in the present tool
118 #save.image(paste("probmetab","RData",sep="."))
119