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comparison transformation_wrapper.R @ 0:eacea1349a7c draft

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
author ethevenot
date Fri, 29 Jul 2016 12:11:01 -0400
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children d9e05021553c
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-1:000000000000 0:eacea1349a7c
1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
2
3
4 library(batch) ## parseCommandArgs
5
6 source_local <- function(fname){
7 argv <- commandArgs(trailingOnly = FALSE)
8 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
9 source(paste(base_dir, fname, sep="/"))
10 }
11
12 source_local("transformation_script.R")
13
14 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
15
16
17 #### Start_of_tested_code <- function() {}
18
19
20 ##------------------------------
21 ## Initializing
22 ##------------------------------
23
24 ## options
25 ##--------
26
27 strAsFacL <- options()[["stringsAsFactors"]]
28 options(stringsAsFactors=FALSE)
29
30 ## constants
31 ##----------
32
33 modNamC <- "Transformation" ## module name
34 metVc <- c("log2", "log10") ## available methods
35
36 topEnvC <- environment()
37 flagC <- "\n"
38
39 ## functions
40 ##----------
41
42 flgF <- function(tesC,
43 envC = topEnvC,
44 txtC = NA) { ## management of warning and error messages
45
46 tesL <- eval(parse(text = tesC), envir = envC)
47
48 if(!tesL) {
49
50 sink(NULL)
51 stpTxtC <- ifelse(is.na(txtC),
52 paste0(tesC, " is FALSE"),
53 txtC)
54
55 stop(stpTxtC,
56 call. = FALSE)
57
58 }
59
60 } ## flgF
61
62 ## log file
63 ##---------
64
65 sink(argVc[["information"]])
66
67 cat("\nStart of the '", modNamC, "' module: ",
68 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
69
70 ## loading
71 ##--------
72
73 datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
74 check.names = FALSE,
75 header = TRUE,
76 row.names = 1,
77 sep = "\t")))
78
79 metC <- argVc[["method"]]
80
81 ## checking
82 ##---------
83
84 flgF("metC %in% metVc", txtC = paste0("Transformation method must be either '", paste(metVc, collapse = "', '"), "'"))
85
86
87 ##------------------------------
88 ## Computation
89 ##------------------------------
90
91
92 datMN <- transformF(datMN = datMN, ## dataMatrix
93 metC = metC) ## transformation method
94
95
96 ##------------------------------
97 ## Ending
98 ##------------------------------
99
100
101 ## saving
102 ##-------
103
104 datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
105 as.data.frame(t(datMN)))
106 write.table(datDF,
107 file = argVc[["dataMatrix_out"]],
108 quote = FALSE,
109 row.names = FALSE,
110 sep = "\t")
111
112 ## ending
113 ##-------
114
115 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
116 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
117
118 sink()
119
120 options(stringsAsFactors = strAsFacL)
121
122
123 #### End_of_tested_code <- function() {}
124
125
126 rm(list = ls())