annotate CAMERA.r @ 2:2591056df814 draft

planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
author lecorguille
date Sun, 10 Apr 2016 08:14:07 -0400
parents
children 9a1a72ee9418
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
1 #!/usr/bin/env Rscript
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
2 # CAMERA.r version="2.2.1"
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
3
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
4
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
5
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
6 # ----- PACKAGE -----
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
7 cat("\tPACKAGE INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
8
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
9 #pkgs=c("xcms","batch")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
10 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
11 for(p in pkgs) {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
12 suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
13 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
14 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
15 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
16
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
17 cat("\n\n");
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
18
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
19
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
20
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
21 # ----- ARGUMENTS -----
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
22 cat("\tARGUMENTS INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
23
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
24 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
25 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
26
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
27 cat("\n\n");
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
28
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
29
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
30 # ----- PROCESSING INFILE -----
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
31 cat("\tINFILE PROCESSING INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
32
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
33 #image is an .RData file necessary to use xset variable given by previous tools
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
34 if (!is.null(listArguments[["image"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
35 load(listArguments[["image"]]); listArguments[["image"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
36 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
37
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
38 if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
39 load(listArguments[["image_pos"]])
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
40 xaP=xa
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
41 if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
42
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
43 diffrepP=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
44 if (exists("diffrep")) diffrepP=diffrep
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
45
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
46 load(listArguments[["image_neg"]])
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
47 xaN=xa
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
48 if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
49
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
50 diffrepN=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
51 if (exists("diffrep")) diffrepN=diffrep
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
52 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
53
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
54
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
55 cat("\n\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
56
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
57
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
58 # ----- ARGUMENTS PROCESSING -----
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
59 cat("\tARGUMENTS PROCESSING INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
60
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
61 # Save arguments to generate a report
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
62 if (!exists("listOFlistArguments")) listOFlistArguments=list()
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
63 listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
64
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
65
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
66 #saving the commun parameters
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
67 thefunction = listArguments[["xfunction"]]
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
68 listArguments[["xfunction"]]=NULL #delete from the list of arguments
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
69
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
70 xsetRdataOutput = paste(thefunction,"RData",sep=".")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
71 if (!is.null(listArguments[["xsetRdataOutput"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
72 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
73 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
74
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
75 rplotspdf = "Rplots.pdf"
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
76 if (!is.null(listArguments[["rplotspdf"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
77 rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
78 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
79
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
80 dataMatrixOutput = "dataMatrix.tsv"
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
81 if (!is.null(listArguments[["dataMatrixOutput"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
82 dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
83 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
84
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
85 variableMetadataOutput = "variableMetadata.tsv"
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
86 if (!is.null(listArguments[["variableMetadataOutput"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
87 variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
88 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
89
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
90 if (!is.null(listArguments[["new_file_path"]])){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
91 new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
92 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
93
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
94 #Import the different functions
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
95 source_local("lib.r")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
96
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
97 # We unzip automatically the chromatograms from the zip files.
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
98 if (thefunction == "annotatediff") {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
99 if(exists("zipfile") && (zipfile!="")) {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
100 suppressWarnings(unzip(zipfile, unzip="unzip"))
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
101 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
102 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
103
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
104
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
105 #addition of xset object to the list of arguments in the first position
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
106 if (exists("xset") != 0){
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
107 listArguments=append(list(xset), listArguments)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
108 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
109
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
110 cat("\n\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
111
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
112
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
113
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
114
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
115 # ----- PROCESSING INFO -----
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
116 cat("\tMAIN PROCESSING INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
117
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
118 #change the default display settings
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
119 pdf(file=rplotspdf, width=16, height=12)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
120
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
121
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
122 if (thefunction %in% c("annotatediff")) {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
123 results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
124 xa=results_list[["xa"]]
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
125 diffrep=results_list[["diffrep"]]
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
126 variableMetadata=results_list[["variableMetadata"]]
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
127
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
128 cat("\n\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
129 cat("\tXSET OBJECT INFO\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
130 print(xa)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
131 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
132
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
133 if (thefunction %in% c("combinexsAnnos")) {
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
134 cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
135 }
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
136
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
137 dev.off()
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
138
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
139
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
140 #saving R data in .Rdata file to save the variables used in the present tool
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
141 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
142 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
143
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
144 cat("\n\n")
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
145
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
146 cat("\tDONE\n")