Mercurial > repos > marie-tremblay-metatoul > nmr_preprocessing

comparison ReadFids_wrapper.R @ 2:5e64657b4fe5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
author lecorguille
date Wed, 28 Mar 2018 08:05:12 -0400
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1:cbea5e9fd0b4 2:5e64657b4fe5
1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
2
3 ## 08122016_ReadFids_wrapper.R
4 ## Manon Martin
5 ## manon.martin@uclouvain.be
6
7 ##======================================================
8 ##======================================================
9 # Preamble
10 ##======================================================
11 ##======================================================
12
13 runExampleL <- FALSE
14
15
16 ##------------------------------
17 ## Options
18 ##------------------------------
19 strAsFacL <- options()$stringsAsFactors
20 options(stringsAsFactors = FALSE)
21 options(warn=1)
22
23 ##------------------------------
24 ## Libraries laoding
25 ##------------------------------
26 library(batch)
27 library(ggplot2)
28 library(gridExtra)
29 library(reshape2)
30
31
32 # R script call
33 source_local <- function(fname)
34 {
35 argv <- commandArgs(trailingOnly = FALSE)
36 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
37 source(paste(base_dir, fname, sep="/"))
38 }
39 #Import the different functions
40 source_local("ReadFids_script.R")
41 source_local("DrawFunctions.R")
42 ##------------------------------
43 ## Errors ?????????????????????
44 ##------------------------------
45
46
47 ##------------------------------
48 ## Constants
49 ##------------------------------
50 topEnvC <- environment()
51 flagC <- "\n"
52
53
54 ##------------------------------
55 ## Script
56 ##------------------------------
57 if(!runExampleL)
58 argLs <- parseCommandArgs(evaluate=FALSE)
59
60 sink(argLs$logOut)
61
62 ##======================================================
63 ##======================================================
64 ## Parameters Loading
65 ##======================================================
66 ##======================================================
67
68 ## Inputs
69 # Path
70 ## Bruker FIDs
71 fileType="Bruker"
72 zipfile= argLs[["fidzipfile"]]
73 directory=unzip(zipfile, list=F)
74 path=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
75
76
77 # other inputs from ReadFids
78 l = argLs[["title_line"]]
79 subdirs <- argLs[["subdirectories"]]
80 dirs.names <- argLs[["dirs_names"]]
81
82
83 # Outputs
84 # dataMatrix <- argLs[["dataMatrix"]]
85 # sampleMetadata <- argLs[["sampleMetadata"]]
86 logOut <- argLs[["logOut"]]
87 nomGraphe <- argLs[["graphOut"]]
88
89
90
91 ## Checking arguments
92 ##-------------------
93 error.stock <- "\n"
94
95 if(length(error.stock) > 1)
96 stop(error.stock)
97
98
99
100 ##======================================================
101 ##======================================================
102 ## Computation
103 ##======================================================
104 ##======================================================
105 sink(logOut,append=TRUE)
106
107 if(length(warnings())>0){ # or !is.null(warnings())
108 print("something happened")
109 }
110
111 ## Starting
112 cat("\nStart of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), "\n\n", sep = "")
113
114 outputs <- ReadFids(path = path, l=l, subdirs = subdirs, dirs.names = dirs.names)
115
116 data_matrix <- outputs[["Fid_data"]] # Data matrix
117 data_sample <- outputs[["Fid_info"]] # Sample metadata
118
119
120
121 pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
122 title = "Raw FID data"
123 DrawSignal(data_matrix, subtype = "stacked",
124 ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
125 xlab = "Frequency", num.stacked = 4,
126 main = title, createWindow=FALSE)
127 invisible(dev.off())
128
129 ##======================================================
130 ##======================================================
131 ## Saving
132 ##======================================================
133 ##======================================================
134
135 # Data matrix
136 write.table(data_matrix,file=argLs$dataMatrix, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
137
138 # Sample metadata
139 write.table(data_sample,file=argLs$sampleMetadata, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
140
141 # log file
142 # write.table(t(data.frame(argLs)), file = argLs$logOut, col.names = FALSE, quote=FALSE)
143
144 # input arguments
145 cat("\n INPUT and OUTPUT ARGUMENTS :\n")
146
147 argLs
148
149 ## Ending
150
151 cat("\nEnd of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), sep = "")
152
153 sink()
154
155
156 options(stringsAsFactors = strAsFacL)
157
158 rm(list = ls())