Mercurial > repos > lecorguille > ipo

comparison ipo4xcmsSet.r @ 0:ac5f2936575b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
author lecorguille
date Thu, 03 Aug 2017 06:00:00 -0400
parents
children ae8de756dfcf
comparison
equal deleted inserted replaced
-1:000000000000 0:ac5f2936575b
1 #!/usr/bin/env Rscript
2 #Authors Gildas Le Corguille and Yann Guitton
3
4
5 # ----- LOG FILE -----
6 log_file=file("log.txt", open = "wt")
7 sink(log_file)
8 sink(log_file, type = "output")
9
10
11 # ----- PACKAGE -----
12 options(bitmapType='cairo')
13 cat("\tPACKAGE INFO\n")
14 #pkgs=c("xcms","batch")
15 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch")
16 for(pkg in pkgs) {
17 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
18 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
19 }
20 source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
21 cat("\n\n");
22
23
24
25
26
27 # ----- ARGUMENTS -----
28 cat("\tARGUMENTS INFO\n")
29 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
30 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
31
32 cat("\n\n");
33
34
35 # ----- ARGUMENTS PROCESSING -----
36 cat("\tINFILE PROCESSING INFO\n")
37
38
39 #Import the different functions
40 source_local("lib.r")
41
42 cat("\n\n")
43
44 #Import the different functions
45
46 # ----- PROCESSING INFILE -----
47 cat("\tARGUMENTS PROCESSING INFO\n")
48
49 xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".")
50 if (!is.null(listArguments[["xsetRdataOutput"]])){
51 xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
52 }
53
54 parametersOutput = "parametersOutput.tsv"
55 if (!is.null(listArguments[["parametersOutput"]])){
56 parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL
57 }
58
59 samplebyclass = 2
60 if (!is.null(listArguments[["samplebyclass"]])){
61 samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL
62 }
63
64 #necessary to unzip .zip file uploaded to Galaxy
65 #thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
66
67
68 if (!is.null(listArguments[["zipfile"]])){
69 zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
70 }
71
72
73 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
74 singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL
75 singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL
76 }
77
78 # single file case
79 #@TODO: need to be refactoring
80 if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
81 if(!file.exists(singlefile_galaxyPath)){
82 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
83 print(error_message); stop(error_message)
84 }
85
86 cwd=getwd()
87 dir.create("raw")
88 setwd("raw")
89 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
90 setwd(cwd)
91
92 directory = "raw"
93
94 }
95
96 # We unzip automatically the chromatograms from the zip files.
97 if(exists("zipfile") && (zipfile!="")) {
98 if(!file.exists(zipfile)){
99 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
100 print(error_message)
101 stop(error_message)
102 }
103
104 #list all file in the zip file
105 #zip_files=unzip(zipfile,list=T)[,"Name"]
106
107 # Because IPO only want raw data in its working directory
108 dir.create("ipoworkingdir")
109 setwd("ipoworkingdir")
110
111 #unzip
112 suppressWarnings(unzip(zipfile, unzip="unzip"))
113
114 #get the directory name
115 filesInZip=unzip(zipfile, list=T);
116 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
117 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
118 directory = "."
119 if (length(directories) == 1) directory = directories
120
121 cat("files_root_directory\t",directory,"\n")
122
123
124 }
125
126 #addition of the directory to the list of arguments in the first position
127 checkXmlStructure(directory)
128 checkFilesCompatibilityWithXcms(directory)
129
130 cat("\n\n")
131
132
133
134
135
136
137 # ----- MAIN PROCESSING INFO -----
138 cat("\tMAIN PROCESSING INFO\n")
139
140
141 xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass)
142
143
144
145 cat("\n\n")
146
147
148 # ----- EXPORT -----
149
150 cat("\tXSET OBJECT INFO\n")
151 print(xset)
152 #delete the parameters to avoid the passage to the next tool in .RData image
153
154
155 #saving R data in .Rdata file to save the variables used in the present tool
156 objects2save = c("xset","zipfile")
157 save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
158
159 cat("\n\n")
160
161
162 cat("\tDONE\n")
163