Mercurial > repos > ethevenot > checkformat

annotate checkformat_wrapper.R @ 0:059eb452931e draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
author ethevenot
date Tue, 24 Oct 2017 08:44:02 -0400
parents
children b642f4f87022
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059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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1 #!/usr/bin/env Rscript
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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)
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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("checkformat_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 <- "Check Format" ## module name
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31 ## log file
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32 ##---------
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34 sink(argVc["information"])
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36 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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40 ##------------------------------
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41 ## Computation
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42 ##------------------------------
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45 resLs <- readAndCheckF(argVc["dataMatrix_in"],
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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46 argVc["sampleMetadata_in"],
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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47 argVc["variableMetadata_in"])
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48 chkL <- resLs[["chkL"]]
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51 ##------------------------------
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52 ## Ending
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53 ##------------------------------
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56 if(chkL) {
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58 cat("\nTable formats are OK; enjoy your analyses!\n", sep="")
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60 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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61 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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63 cat("\n\n\n============================================================================")
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64 cat("\nAdditional information about the call:\n")
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65 cat("\n1) Parameters:\n")
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66 print(cbind(value = argVc))
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68 cat("\n2) Session Info:\n")
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69 sessioninfo <- sessionInfo()
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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70 cat(sessioninfo$R.version$version.string,"\n")
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71 cat("Main packages:\n")
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72 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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73 cat("Other loaded packages:\n")
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74 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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76 cat("============================================================================\n")
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78 sink()
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80 } else {
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82 cat("\n\n\n============================================================================")
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83 cat("\nAdditional information about the call:\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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84 cat("\n1) Parameters:\n")
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85 print(cbind(value = argVc))
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86
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87 cat("\n2) Session Info:\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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88 sessioninfo <- sessionInfo()
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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89 cat(sessioninfo$R.version$version.string,"\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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90 cat("Main packages:\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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91 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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92 cat("Other loaded packages:\n")
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93 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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95 cat("============================================================================\n")
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97 sink()
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98 stop("Please check the generated 'information' file")
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99
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100 }
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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101
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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102 ## closing
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
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103 ##--------
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104
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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105 options(stringsAsFactors = strAsFacL)
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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parents:
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106
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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107 rm(list = ls())