Mercurial > repos > eschen42 > w4mclassfilter
annotate w4mclassfilter_wrapper.R @ 0:bab3a658f74e draft
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author | eschen42 |
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date | Tue, 09 May 2017 18:34:35 -0400 |
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children | 23c6d271def9 |
rev | line source |
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1 #!/usr/bin/env Rscript |
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2 |
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3 library(batch) ## parseCommandArgs |
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4 |
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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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10 |
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11 ##------------------------------ |
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12 ## Initializing |
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13 ##------------------------------ |
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14 |
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15 ## options |
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16 ##-------- |
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17 |
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18 strAsFacL <- options()$stringsAsFactors |
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19 options(stringsAsFactors = FALSE) |
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20 |
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21 ## libraries |
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22 ##---------- |
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23 |
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24 suppressMessages(library(w4mclassfilter)) |
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25 |
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26 if(packageVersion("w4mclassfilter") < "0.98.0") |
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27 stop("Please use 'w4mclassfilter' versions of 0.98.0 and above") |
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28 |
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29 ## constants |
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30 ##---------- |
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31 |
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32 modNamC <- "w4mclassfilter" ## module name |
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33 |
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34 topEnvC <- environment() |
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35 flgC <- "\n" |
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36 |
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37 ## functions |
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38 ##---------- |
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39 |
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40 flgF <- function(tesC, |
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41 envC = topEnvC, |
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42 txtC = NA) { ## management of warning and error messages |
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43 |
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44 tesL <- eval(parse(text = tesC), envir = envC) |
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45 |
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46 if(!tesL) { |
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47 |
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48 #sink(NULL) |
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49 stpTxtC <- ifelse(is.na(txtC), |
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50 paste0(tesC, " is FALSE"), |
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51 txtC) |
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52 |
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53 stop(stpTxtC, |
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54 call. = FALSE) |
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55 |
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56 } |
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57 |
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58 } ## flgF |
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59 |
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60 |
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61 ## log file |
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62 ##--------- |
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63 |
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64 information <- as.character(argVc["information"]) |
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65 |
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66 #sink(information) |
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67 |
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68 my_print <- function(x, ...) { cat(c(x, ...))} |
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69 |
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70 my_print("\nStart of the '", modNamC, "' Galaxy module call: ", |
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71 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") |
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72 |
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73 ## arguments |
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74 ##---------- |
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75 |
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76 # files |
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77 |
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78 dataMatrix_in <- as.character(argVc["dataMatrix_in"]) |
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79 dataMatrix_out <- as.character(argVc["dataMatrix_out"]) |
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80 |
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81 sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) |
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82 sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) |
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83 |
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84 variableMetadata_in <- as.character(argVc["variableMetadata_in"]) |
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85 variableMetadata_out <- as.character(argVc["variableMetadata_out"]) |
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86 |
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87 # other parameters |
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88 |
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89 sampleclassNames <- as.character(argVc["sampleclassNames"]) |
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90 # if (sampleclassNames == "NONE_SPECIFIED") { |
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91 # sampleclassNames <- as.character(c()) |
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92 # |
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93 # } else { |
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94 # sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] |
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95 # } |
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96 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] |
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97 inclusive <- as.logical(argVc["inclusive"]) |
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98 # print(sprintf("inclusive = '%s'", as.character(inclusive))) |
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99 classnameColumn <- as.character(argVc["classnameColumn"]) |
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100 samplenameColumn <- as.character(argVc["samplenameColumn"]) |
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101 |
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102 ##------------------------------ |
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103 ## Computation |
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104 ##------------------------------ |
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105 |
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106 result <- w4m_filter_by_sample_class( |
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107 dataMatrix_in = dataMatrix_in |
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108 , sampleMetadata_in = sampleMetadata_in |
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109 , variableMetadata_in = variableMetadata_in |
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110 , dataMatrix_out = dataMatrix_out |
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111 , sampleMetadata_out = sampleMetadata_out |
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112 , variableMetadata_out = variableMetadata_out |
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113 , classes = sampleclassNames |
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114 , include = inclusive |
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115 , class_column = classnameColumn |
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116 , samplename_column = samplenameColumn |
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117 , failure_action = my_print |
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118 ) |
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119 |
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120 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", |
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121 as.character(result), "\n", sep = "") |
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122 |
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123 ##-------- |
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124 ## Closing |
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125 ##-------- |
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126 |
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127 my_print("\nEnd of '", modNamC, "' Galaxy module call: ", |
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128 as.character(Sys.time()), "\n", sep = "") |
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129 |
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130 #sink() |
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131 |
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132 if (!file.exists(dataMatrix_out)) { |
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133 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) |
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134 }# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } |
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135 |
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136 if (!file.exists(variableMetadata_out)) { |
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137 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) |
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138 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } |
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139 |
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140 if (!file.exists(sampleMetadata_out)) { |
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141 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) |
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142 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } |
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143 |
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144 if( !result ) { |
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145 stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) |
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146 } |
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147 |
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148 rm(list = ls()) |