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annotate w4mclstrpeakpics_wrapper.R @ 0:caf0ce49b638 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
author eschen42
date Sun, 18 Jun 2017 23:25:58 -0400
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children 17356c5fe43e
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caf0ce49b638 planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
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1 #!/usr/bin/env Rscript
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3 library(batch) ## parseCommandArgs
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5 ########
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6 # MAIN #
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7 ########
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8
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9 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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11 ##------------------------------
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12 ## Initializing
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13 ##------------------------------
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15 ## options
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16 ##--------
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18 strAsFacL <- options()$stringsAsFactors
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19 options(stringsAsFactors = FALSE)
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21 ## libraries
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22 ##----------
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24 # begin HACK - suppress " Can't find a usable init.tcl ... probably means that Tcl wasn't installed properly" issue
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25 library("gsubfn")
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26 options(gsubfn.engine = "R")
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27 # end HACK
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29 r_package_archive <- as.character(argVc["r_package_archive"])
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30 install.packages(r_package_archive, repos = NULL, type = "source")
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31 suppressMessages( library("w4mclstrpeakpics") )
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33 ## constants
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34 ##----------
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36 modNamC <- "w4mclsltrpeakpics" ## module name
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38 topEnvC <- environment()
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39 flgC <- "\n"
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40
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41 ## functions
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42 ##----------
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45 ## log file
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46 ##---------
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47
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48 my_print <- function(x, ...) { cat(c(x, ...))}
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49
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50 my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
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51 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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52
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53 ## arguments
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54 ##----------
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55
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56 # files
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57
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58 output_pdf <- as.character(argVc["output_pdf"])
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59 output_tsv <- as.character(argVc["output_tsv"])
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60 output_rdata <- as.character(argVc["output_rdata"])
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61 data_matrix_path <- as.character(argVc["data_matrix_path"])
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62 variable_metadata_path <- as.character(argVc["variable_metadata_path"])
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63 sample_metadata_path <- as.character(argVc["sample_metadata_path"])
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64
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65 # other parameters
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66
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67 sample_selector_column_name <- as.character(argVc["sample_selector_column_name"])
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68 sample_selector_value <- as.character(argVc["sample_selector_value"])
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69
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70 ##------------------------------
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71 ## Computation
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72 ##------------------------------
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73
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74 # from 'demo(error.catching)'
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75 tryCatch.W.E <- function(expr) {
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76 W <- NULL
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77 w.handler <- function(w){
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78 # warning handler
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79 W <<- w
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80 invokeRestart("muffleWarning")
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81 }
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82 list(
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83 value = withCallingHandlers(
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84 tryCatch(expr, error = function(e) e)
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85 , warning = w.handler
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86 )
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87 , warning = W
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88 )
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89 }
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90
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91 result <- cluster_peak_assessment(
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92 sample_selector_column_name = sample_selector_column_name
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93 , sample_selector_value = sample_selector_value
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94 , sample_metadata_path = sample_metadata_path
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95 , variable_metadata_path = variable_metadata_path
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96 , data_matrix_path = data_matrix_path
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97 , output_pdf = output_pdf
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98 , output_tsv = output_tsv
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99 , output_rdata = output_rdata
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100 , failure_action = my_print
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101 )
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102
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103
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104 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
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105 as.character(result), "\n", sep = "")
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106
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107 ##--------
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108 ## Closing
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109 ##--------
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110
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111 my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
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112 as.character(Sys.time()), "\n", sep = "")
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113
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114 #sink()
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115
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116 if (!file.exists(output_pdf)) {
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117 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_pdf))
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118 }
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119
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120 if (!file.exists(output_tsv)) {
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121 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_tsv))
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122 }
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123
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124 if (!file.exists(output_rdata)) {
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125 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_rdata))
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126 }
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127
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128 # 'stop' causes Rscript to return a non-zero exit code
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129 if( !result ) {
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130 stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
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131 }
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132
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133 # exit with status code zero
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134 q(save = "no", status = 0, runLast = FALSE)