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annotate transformation_wrapper.R @ 1:d971449245b1 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
author ethevenot
date Wed, 28 Feb 2018 09:20:37 -0500
parents c7b8e82af08e
children
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c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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1 #!/usr/bin/env Rscript
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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3 library(batch) ## parseCommandArgs
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5 # Constants
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6 argv <- commandArgs(trailingOnly = FALSE)
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
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8 prog.name <- basename(script.path)
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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10 # Print help
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11 if (length(grep('-h', argv)) >0) {
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12 cat("Usage:", prog.name,
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13 "dataMatrix_in myDataMatrixInput.tsv",
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14 "method log2|log10|sqrt",
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15 "dataMatrix_out myDataMatrixOutput.tsv",
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16 "information information.txt",
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17 "\n")
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18 quit(status = 0)
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19 }
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21 source_local <- function(fname){
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22 argv <- commandArgs(trailingOnly = FALSE)
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23 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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24 source(paste(base_dir, fname, sep="/"))
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25 }
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27 source_local("transformation_script.R")
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29 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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32 ##------------------------------
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33 ## Initializing
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34 ##------------------------------
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36 ## options
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37 ##--------
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39 strAsFacL <- options()[["stringsAsFactors"]]
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40 options(stringsAsFactors=FALSE)
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42 ## constants
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43 ##----------
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45 modNamC <- "Transformation" ## module name
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48 ## log file
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49 ##---------
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51 sink(argVc[["information"]])
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53 cat("\nStart of the '", modNamC, "' module: ",
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54 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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56 ## loading
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57 ##--------
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58
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59 datMN <- t(as.matrix(read.table(argVc[["dataMatrix_in"]],
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60 check.names = FALSE,
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61 header = TRUE,
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62 row.names = 1,
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63 sep = "\t")))
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65 metC <- argVc[["method"]]
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68 ##------------------------------
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69 ## Computation
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70 ##------------------------------
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73 datMN <- transformF(datMN = datMN, ## dataMatrix
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74 metC = metC) ## transformation method
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77 ##------------------------------
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78 ## Ending
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79 ##------------------------------
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82 ## saving
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83 ##-------
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85 datDF <- cbind.data.frame(dataMatrix = colnames(datMN),
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86 as.data.frame(t(datMN)))
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87 write.table(datDF,
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88 file = argVc[["dataMatrix_out"]],
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89 quote = FALSE,
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90 row.names = FALSE,
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91 sep = "\t")
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93 ## ending
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94 ##-------
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95
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96 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
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97 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
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99 cat("\n\n\n============================================================================")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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100 cat("\nAdditional information about the call:\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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101 cat("\n1) Parameters:\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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102 print(cbind(value = argVc))
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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103
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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104 cat("\n2) Session Info:\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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105 sessioninfo <- sessionInfo()
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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106 cat(sessioninfo$R.version$version.string,"\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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107 cat("Main packages:\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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108 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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109 cat("Other loaded packages:\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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110 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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111
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
parents:
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112 cat("============================================================================\n")
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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113
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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114 sink()
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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115
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
ethevenot
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116 options(stringsAsFactors = strAsFacL)
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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117
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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118
c7b8e82af08e planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 308ae36af707ede5697d1b8a0c93f8b5b68872cf
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119 rm(list = ls())