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