annotate ipo4xcmsSet.r @ 6:03fdfbd914ab draft

planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
author lecorguille
date Thu, 30 Mar 2017 11:27:09 -0400
parents
children 80de755766a8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
1 #!/usr/bin/env Rscript
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
2 #Authors Gildas Le Corguille and Yann Guitton
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
3
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
4
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
5 # ----- LOG FILE -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
6 log_file=file("log.txt", open = "wt")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
7 sink(log_file)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
8 sink(log_file, type = "output")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
9
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
10
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
11 # ----- PACKAGE -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
12 options(bitmapType='cairo')
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
13 cat("\tPACKAGE INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
14 #pkgs=c("xcms","batch")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
16 for(pkg in pkgs) {
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
17 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
18 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
19 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
20 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
21 cat("\n\n");
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
22
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
23
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
24
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
25
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
26
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
27 # ----- ARGUMENTS -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
28 cat("\tARGUMENTS INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
29 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
30 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
31
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
32 cat("\n\n");
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
33
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
34
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
35 # ----- ARGUMENTS PROCESSING -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
36 cat("\tINFILE PROCESSING INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
37
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
38
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
39 #Import the different functions
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
40 source_local("lib.r")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
41
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
42 cat("\n\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
43
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
44 #Import the different functions
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
45
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
46 # ----- PROCESSING INFILE -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
47 cat("\tARGUMENTS PROCESSING INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
48
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
49 xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
50 if (!is.null(listArguments[["xsetRdataOutput"]])){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
51 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
52 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
53
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
54 parametersOutput = "parametersOutput.tsv"
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
55 if (!is.null(listArguments[["parametersOutput"]])){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
56 parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
57 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
58
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
59 samplebyclass = 2
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
60 if (!is.null(listArguments[["samplebyclass"]])){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
61 samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
62 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
63
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
64 #necessary to unzip .zip file uploaded to Galaxy
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
65 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
66
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
67
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
68 if (!is.null(listArguments[["zipfile"]])){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
69 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
70 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
71
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
72
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
73 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
74 singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
75 singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
76 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
77
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
78 # single file case
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
79 #@TODO: need to be refactoring
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
80 if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
81 if(!file.exists(singlefile_galaxyPath)){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
82 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
83 print(error_message); stop(error_message)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
84 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
85
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
86 cwd=getwd()
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
87 dir.create("raw")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
88 setwd("raw")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
89 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
90 setwd(cwd)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
91
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
92 directory = "raw"
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
93
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
94 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
95
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
96 # We unzip automatically the chromatograms from the zip files.
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
97 if(exists("zipfile") && (zipfile!="")) {
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
98 if(!file.exists(zipfile)){
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
99 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
100 print(error_message)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
101 stop(error_message)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
102 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
103
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
104 #list all file in the zip file
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
105 #zip_files=unzip(zipfile,list=T)[,"Name"]
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
106
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
107 # Because IPO only want raw data in its working directory
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
108 dir.create("ipoworkingdir")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
109 setwd("ipoworkingdir")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
110 file.symlink(zipfile, ".")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
111
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
112 #unzip
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
113 suppressWarnings(unzip(zipfile, unzip="unzip"))
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
114
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
115 #get the directory name
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
116 filesInZip=unzip(zipfile, list=T);
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
117 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
118 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
119 directory = "."
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
120 if (length(directories) == 1) directory = directories
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
121
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
122 cat("files_root_directory\t",directory,"\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
123
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
124 file.remove(zipfile)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
125
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
126
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
127 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
128
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
129 #addition of the directory to the list of arguments in the first position
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
130 checkXmlStructure(directory)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
131 checkFilesCompatibilityWithXcms(directory)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
132
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
133 cat("\n\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
134
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
135
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
136
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
137
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
138
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
139
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
140 # ----- MAIN PROCESSING INFO -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
141 cat("\tMAIN PROCESSING INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
142
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
143
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
144 xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
145
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
146
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
147
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
148 cat("\n\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
149
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
150
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
151 # ----- EXPORT -----
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
152
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
153 cat("\tXSET OBJECT INFO\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
154 print(xset)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
155 #delete the parameters to avoid the passage to the next tool in .RData image
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
156
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
157
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
158 #saving R data in .Rdata file to save the variables used in the present tool
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
159 objects2save = c("xset","zipfile")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
160 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
161
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
162 cat("\n\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
163
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
164
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
165 cat("\tDONE\n")
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents:
diff changeset
166