Mercurial > repos > ethevenot > profia

comparison profia_wrapper.R @ 0:39ccace77270 draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 2757590af8c7ba9833ba3bebd7da7f96b20d1128-dirty
author ethevenot
date Sun, 26 Mar 2017 17:37:12 -0400
parents
children 4753e64cf694
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-1:000000000000 0:39ccace77270
1 #!/usr/bin/env Rscript
2
3 library(batch) ## parseCommandArgs
4
5 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
6
7 ##------------------------------
8 ## Initializing
9 ##------------------------------
10
11
12 ## libraries
13 ##----------
14
15 suppressMessages(library(proFIA))
16
17
18 ## constants
19 ##----------
20
21 modNamC <- "proFIA" ## module name
22
23
24 ## log file
25 ##---------
26
27 sink(argVc["information"])
28
29 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
30 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
31
32
33 ## arguments
34 ##----------
35
36
37 if("zipfile" %in% names(argVc)) {
38
39 zipfile <- argVc["zipfile"]
40
41 ## We unzip automatically the raw files from the zip file
42
43 if(exists("zipfile") && (zipfile!="")) {
44 if(!file.exists(zipfile)){
45 error_message=paste("Cannot access the Zip file:", zipfile)
46 print(error_message)
47 stop(error_message)
48 }
49
50 ## unzip
51
52 suppressWarnings(unzip(zipfile, unzip="unzip"))
53
54 ## get the directory name
55
56 filesInZip=unzip(zipfile, list=T);
57 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
58 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
59 directory = "."
60 if (length(directories) == 1) directory = directories
61
62 cat("files_root_directory\t",directory,"\n")
63
64 }
65
66 } else if ("library" %in% names(argVc)) {
67
68 directory <- argVc["library"]
69
70 if(!file.exists(directory)) {
71
72 error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
73 print(error_message)
74 stop(error_message)
75
76 }
77
78 } else {
79
80 error_message <- "No zipfile nor input library available"
81 print(error_message)
82 stop(error_message)
83
84 }
85
86 ##------------------------------
87 ## Computations
88 ##------------------------------
89
90
91 optWrnN <- options()$warn
92 options(warn = -1)
93
94 stpI <- 1
95
96 cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
97
98 fiaset <- proFIAset(directory,
99 ppm = as.numeric(argVc["ppmN"]),
100 parallel = FALSE)
101
102 stpI <- stpI + 1
103
104 cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
105
106 fiaset <- group.FIA(fiaset,
107 ppmGroup = as.numeric(argVc["ppmGroupN"]),
108 fracGroup = as.numeric(argVc["fracGroupN"]))
109
110 stpI <- stpI + 1
111
112 cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
113
114 fiaset <- makeDataMatrix(fiaset,
115 maxo = FALSE)
116
117 stpI <- stpI + 1
118
119 kI <- as.integer(argVc["kI"])
120
121 if(kI > 0) {
122
123 cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")
124
125 fiaset <- imputeMissingValues.WKNN_TN(fiaset,
126 k = kI)
127
128 stpI <- stpI + 1
129 }
130
131 options(warn = optWrnN)
132
133
134 ##------------------------------
135 ## Ending
136 ##------------------------------
137
138
139 ## Plotting
140 ##---------
141
142 cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
143
144 pdf(argVc["figure"])
145
146 plot(fiaset)
147
148 dev.off()
149
150 stpI <- stpI + 1
151
152 ## Printing
153 ##---------
154
155 cat("\n", stpI, ") Printing ('show'):\n", sep = "")
156
157 fiaset
158
159 stpI <- stpI + 1
160
161 ## Exporting
162 ##----------
163
164 cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
165
166 datMN <- exportDataMatrix(fiaset)
167 samDF <- exportSampleMetadata(fiaset)
168 varDF <- exportVariableMetadata(fiaset)
169
170 if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
171 datDF <- as.data.frame(t(datMN))
172 } else {
173 datDF <- as.data.frame(datMN)
174 }
175 rownames(varDF) <- rownames(datDF)
176
177 datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
178 datDF)
179 write.table(datDF,
180 file = argVc["dataMatrix_out"],
181 quote = FALSE,
182 row.names = FALSE,
183 sep = "\t")
184
185 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
186 samDF)
187 write.table(samDF,
188 file = argVc["sampleMetadata_out"],
189 quote = FALSE,
190 row.names = FALSE,
191 sep = "\t")
192
193 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
194 varDF)
195 write.table(varDF,
196 file = argVc["variableMetadata_out"],
197 quote = FALSE,
198 row.names = FALSE,
199 sep = "\t")
200
201
202 ## Closing
203 ##--------
204
205 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
206 as.character(Sys.time()), "\n", sep = "")
207
208 sink()
209
210 rm(list = ls())