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annotate transformation_wrapper.R @ 2:0ccfc3e15710 draft

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit b0373e2f4702a572450205419e2d64579c24c9ae
author ethevenot
date Tue, 06 Jun 2017 11:55:21 -0400
parents d9e05021553c
children cc0e9eff0de2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d9e05021553c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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1 #!/usr/bin/env Rscript
0
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3 library(batch) ## parseCommandArgs
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5 source_local <- function(fname){
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6 argv <- commandArgs(trailingOnly = FALSE)
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7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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8 source(paste(base_dir, fname, sep="/"))
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9 }
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11 source_local("transformation_script.R")
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13 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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16 ##------------------------------
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17 ## Initializing
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18 ##------------------------------
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20 ## options
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21 ##--------
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23 strAsFacL <- options()[["stringsAsFactors"]]
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24 options(stringsAsFactors=FALSE)
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26 ## constants
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27 ##----------
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29 modNamC <- "Transformation" ## module name
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32 ## log file
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33 ##---------
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35 sink(argVc[["information"]])
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37 cat("\nStart of the '", modNamC, "' module: ",
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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38 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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40 ## loading
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41 ##--------
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43 datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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44 check.names = FALSE,
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45 header = TRUE,
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46 row.names = 1,
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47 sep = "\t")))
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49 metC <- argVc[["method"]]
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52 ##------------------------------
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53 ## Computation
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54 ##------------------------------
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57 datMN <- transformF(datMN = datMN, ## dataMatrix
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58 metC = metC) ## transformation method
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61 ##------------------------------
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62 ## Ending
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63 ##------------------------------
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66 ## saving
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67 ##-------
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69 datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
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70 as.data.frame(t(datMN)))
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71 write.table(datDF,
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72 file = argVc[["dataMatrix_out"]],
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73 quote = FALSE,
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74 row.names = FALSE,
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75 sep = "\t")
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77 ## ending
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78 ##-------
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79
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80 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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81 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
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82
2
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83 cat("\n\n\n============================================================================")
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84 cat("\nAdditional information about the call:\n")
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85 cat("\n1) Parameters:\n")
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86 print(cbind(value = argVc))
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87
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88 cat("\n2) Session Info:\n")
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89 sessioninfo <- sessionInfo()
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90 cat(sessioninfo$R.version$version.string,"\n")
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91 cat("Main packages:\n")
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92 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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93 cat("Other loaded packages:\n")
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94 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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95
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96 cat("============================================================================\n")
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97
0
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98 sink()
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100 options(stringsAsFactors = strAsFacL)
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eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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eacea1349a7c planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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103 rm(list = ls())