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annotate checkformat_wrapper.R @ 3:7f093d78a58c draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 6b7aa0db6cebdb8acfac0a07291647947260a310
author ethevenot
date Thu, 01 Mar 2018 05:09:49 -0500
parents b642f4f87022
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
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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("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: ",
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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"],
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46 argVc["sampleMetadata_in"],
1
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47 argVc["variableMetadata_in"],
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48 as.logical(argVc["makeNameL"]))
0
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51 ##------------------------------
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52 ## Ending
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53 ##------------------------------
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55
1
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56 ## dataMatrix
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57
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58 datMN <- resLs[["datMN"]]
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59 datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
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60 as.data.frame(t(datMN)))
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61 write.table(datDF,
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62 file = argVc[["dataMatrix_out"]],
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63 quote = FALSE,
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64 row.names = FALSE,
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65 sep = "\t")
0
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66
1
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67 ## sampleMetadata
0
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68
1
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69 samDF <- resLs[["samDF"]]
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70 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
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71 samDF)
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72 write.table(samDF,
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73 file = argVc["sampleMetadata_out"],
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74 quote = FALSE,
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75 row.names = FALSE,
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76 sep = "\t")
0
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1
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78 ## variableMetadata
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79
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80 varDF <- resLs[["varDF"]]
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81 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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82 varDF)
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83 write.table(varDF,
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84 file = argVc["variableMetadata_out"],
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85 quote = FALSE,
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86 row.names = FALSE,
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87 sep = "\t")
0
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88
1
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89 if(resLs[["chkL"]]) {
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90
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91 if(resLs[["newL"]]) {
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92
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93 cat("\nWarning: The sample and/or variable names or orders from the input tables have been modified\n(see the information file for details); please use the new output tables for your analyses.\n")
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94
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95 } else {
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96
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97 cat("\nThe input tables have a correct format and can be used for your analyses.\n")
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98
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99 }
0
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100
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101 }
1
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102
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103 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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104 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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105
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106 cat("\n\n\n============================================================================")
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107 cat("\nAdditional information about the call:\n")
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108 cat("\n1) Parameters:\n")
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109 print(cbind(value = argVc))
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110
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111 cat("\n2) Session Info:\n")
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112 sessioninfo <- sessionInfo()
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113 cat(sessioninfo$R.version$version.string,"\n")
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114 cat("Main packages:\n")
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115 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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116 cat("Other loaded packages:\n")
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117 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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118
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119 cat("============================================================================\n")
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120
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121 sink()
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122
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123 if(!resLs[["chkL"]]) {
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124 stop("Please check the generated 'information' file")
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125 }
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126
0
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127
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128 ## closing
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129 ##--------
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131 options(stringsAsFactors = strAsFacL)
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132
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133 rm(list = ls())