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annotate w4mkmeans_wrapper.R @ 0:6ccbe18131a6 draft

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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
author eschen42
date Tue, 08 Aug 2017 15:30:38 -0400
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children 02cafb660b72
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6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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1 #!/usr/bin/env Rscript
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3 # references:
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4 # what this does:
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5 # - [stats::kmeans](https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html)
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6 # - [stats::p.adjust](https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html)
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7 # how this does what it does:
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8 # - [parallel::clusterApply](https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/clusterApply.html)
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9
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10 # invocation:
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11 # Rscript $__tool_directory__/w4mkmeans_wrapper.R \
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12 # tool_directory $__tool_directory__
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13 # data_matrix_path '$dataMatrix_in' \
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14 # variable_metadata_path '$variableMetadata_in' \
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15 # sample_metadata_path '$sampleMetadata_in' \
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16 # kfeatures '$kfeatures' \
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17 # ksamples '$ksamples' \
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18 # iter_max '$iter_max' \
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19 # nstart '$nstart' \
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20 # algorithm '$algorithm' \
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21 # scores '$scores' \
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22 # sampleMetadata_out '$sampleMetadata_out' \
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23 # variableMetadata_out '$variableMetadata_out' \
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24 # slots "\${GALAXY_SLOTS:-1}" \
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25 #
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26 # <inputs>
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27 # <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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28 # <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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29 # <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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30 # <param name="kfeatures" label="K value(s) for features" type="text" value="0" help="Single or min,max value(s) for K for features (variables), or 0 for none." />
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31 # <param name="ksamples" label="K value(s) for samples" type="text" value="0" help="Single or min,max value(s) for K for samples, or 0 for none." />
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32 # <param name="iter_max" label="Max number of iterations" type="text" value="10" help="The maximum number of iterations allowed; default 10." />
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33 # <param name="nstart" label="Number of random sets" type="text" value="1" help="How many random sets should be chosen; default 1." />
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34 # <param name="algorithm" label="Algorithm for clustering" type="select" value = "Hartigan-Wong" help="K-means clustering algorithm, default 'Hartigan-Wong'; alternatives 'Lloyd', 'MacQueen'; 'Forgy' is a synonym for 'Lloyd', see stats::kmeans reference for further info and references.">
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35 # <option value="Hartigan-Wong" selected="TRUE">Hartigan-Wong</option>
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36 # <option value="Lloyd">Lloyd</option>
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37 # <option value="MacQueen">MacQueen</option>
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38 # <option value="Forgy">Forgy</option>
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39 # </param>
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40 # </inputs>
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41 # <outputs>
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42 # <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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43 # <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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44 # </outputs>
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45
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46 ##------------------------
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47 ## libraries for this file
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48 ##------------------------
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49
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50 library(batch) ## for 'parseCommandArgs'
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51
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52 ##-------------------
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53 ## Pre-initialization
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54 ##-------------------
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55
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56 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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57 if ( Reduce( `|`, grepl("tool_directory",names(argVc)) ) ) {
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58 tool_directory <- as.character(argVc["tool_directory"])
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59 } else {
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60 tool_directory <- "."
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61 }
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62 r_path <- function(f) paste( tool_directory, f, sep = "/" )
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63
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64 ##----------------------------------------------------------
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65 ## Computation - source general and module-specific routines
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66 ##----------------------------------------------------------
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67
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68 log_print <- function(x, ...) {
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69 cat(
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70 format(Sys.time(), "%Y-%m-%dT%H:%M:%S%z")
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71 , " "
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72 , c(x, ...)
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73 , "\n"
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74 , sep=""
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75 , file=stderr()
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76 )
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77 }
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78
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79 # log_print(sprintf("tool_directory is %s", tool_directory))
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80
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81 w4m_general_purpose_routines_path <- r_path("w4m_general_purpose_routines.R")
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82 # log_print(sprintf("w4m_general_purpose_routines_path is %s", w4m_general_purpose_routines_path))
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83 if ( ! file.exists(w4m_general_purpose_routines_path) ) {
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84 log_print("cannot find file w4m_general_purpose_routines.R")
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85 q(save = "no", status = 1, runLast = TRUE)
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86 }
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87 # log_print("sourcing ",w4m_general_purpose_routines_path)
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88 source(w4m_general_purpose_routines_path)
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89 if ( ! exists("prepare.data.matrix") ) {
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90 log_print("'prepare.data.matrix' was not read from file w4m_general_purpose_routines.R")
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91 q(save = "no", status = 1, runLast = TRUE)
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92 }
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93
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94 w4mkmeans_routines_path <- r_path("w4mkmeans_routines.R")
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95 # log_print(sprintf("w4mkmeans_routines_path is %s", w4mkmeans_routines_path))
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96 if ( ! file.exists(w4mkmeans_routines_path) ) {
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97 log_print("cannot find file w4mkmeans_routines.R")
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98 q(save = "no", status = 1, runLast = TRUE)
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99 }
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100 # log_print("sourcing ",w4mkmeans_routines_path)
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101 source(w4mkmeans_routines_path)
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102 if ( ! exists("w4mkmeans") ) {
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103 log_print("'w4mkmeans' was not read from file w4mkmeans_routines.R")
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104 q(save = "no", status = 1, runLast = TRUE)
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105 }
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106
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107 ##-----------------------------------------
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108 ## Computation - W4m data-suppport routines
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109 ##-----------------------------------------
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110
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111 # read_data_frame - read a w4m data frame from a tsv, with error handling
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112 # e.g., data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input")
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113 read_data_frame <- function(file_path, kind_string, failure_action = log_print) {
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114 my.env <- new.env()
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115 my.env$success <- FALSE
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116 my.env$msg <- sprintf("no message reading %s", kind_string)
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117 tryCatch(
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118 expr = {
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119 my.env$data <- utils::read.delim( fill = FALSE, file = file_path )
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120 my.env$success <- TRUE
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121 }
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122 , error = function(e) {
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123 my.env$msg <<- sprintf("%s read failed", kind_string)
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124 }
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125 )
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126 if (!my.env$success) {
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127 failure_action(my.env$msg)
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128 }
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129 return (my.env)
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130 }
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131
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132 # write_result - write a w4m data frame to a tsv
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133 write_result <- function(result, file_path, kind_string, failure_action = log_print) {
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134 my.env <- new.env()
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135 my.env$success <- FALSE
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136 my.env$msg <- sprintf("no message writing %s", kind_string)
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diff changeset
137 tryCatch(
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138 expr = {
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139 write.table(
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140 x = result
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141 , sep = "\t"
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142 , file = file_path
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143 , quote = FALSE
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144 , row.names = FALSE
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145 )
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146 my.env$success <- TRUE
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147 }
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148 , error = function(e) {
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149 my.env$msg <<- sprintf("%s write failed", kind_string)
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150 }
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diff changeset
151 )
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152 if (!my.env$success) {
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153 failure_action(my.env$msg)
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154 return (my.env)
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155 }
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156 return (my.env)
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157 }
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158
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159 # read the three input files
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160 read_input_data <- function(env, failure_action = log_print) {
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161 kind_string <- "none"
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162 tryCatch(
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163 expr = {
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164 # read in the sample metadata
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165 kind_string <- "sample metadata input"
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166 smpl_metadata_input_env <-
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167 read_data_frame(
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168 file_path = env$sample_metadata_path
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169 , kind_string = kind_string
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170 , failure_action = failure_action
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171 )
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172 if (!smpl_metadata_input_env$success) {
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173 failure_action(smpl_metadata_input_env$msg)
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174 return ( FALSE )
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175 }
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176 env$sampleMetadata <- smpl_metadata_input_env$data
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177
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178 # read in the variable metadata
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179 kind_string <- "variable metadata input"
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180 vrbl_metadata_input_env <-
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181 read_data_frame(
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182 file_path = env$variable_metadata_path
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183 , kind_string = kind_string
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184 , failure_action = failure_action
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185 )
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186 if (!vrbl_metadata_input_env$success) {
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187 failure_action(vrbl_metadata_input_env$msg)
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188 return ( FALSE )
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189 }
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190 env$variableMetadata <- vrbl_metadata_input_env$data
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191
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192 # read in the data matrix
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193 kind_string <- "data matrix input"
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194 data_matrix_input_env <-
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195 read_data_frame(
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196 file_path = env$data_matrix_path
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197 , kind_string = kind_string
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198 , failure_action = failure_action
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199 )
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200 if (!data_matrix_input_env$success) {
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201 failure_action(data_matrix_input_env$msg)
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202 return ( FALSE )
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203 }
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204 # data frame for dataMatrix has rownames in first column
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205 data_matrix_df <- data_matrix_input_env$data
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206 rownames(data_matrix_df) <- data_matrix_df[,1]
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207 data_matrix <- data_matrix_df[,2:ncol(data_matrix_df)]
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208 env$dataMatrix <- as.matrix(data_matrix)
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209
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210 }
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211 , error = function(e) {
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212 failure_action( sprintf("read_input_data failed for '%s' - %s", kind_string, format_error(e)) )
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213 return ( FALSE )
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214 }
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215 )
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216 return ( TRUE )
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217 }
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218
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219
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220 read_input_failure_action <- function(x, ...) {
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221 log_print("Failure reading input for '", modNamC, "' Galaxy module call")
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222 log_print(x, ...)
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223 }
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224
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225 ##--------------------------
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226 ## Computation - Entry Point
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227 ##--------------------------
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228
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229 ##----------
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230 ## Constants
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231 ##----------
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232
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233 modNamC <- "w4mkmeans" ## module name
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234
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235 ## options
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236 ##--------
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237
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238 # Set the handler for R error-handling
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239 options( show.error.messages = F
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240 , error = function () {
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241 log_print( "Fatal error in '", modNamC, "': ", geterrmessage() )
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242 q( "no", 1, F )
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243 }
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244 , warn = -1
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245 )
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246
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247 # strings as factors? - not by default!
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248 # save old value
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249 strAsFacL <- options()$stringsAsFactors
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250 options(stringsAsFactors = FALSE)
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251
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252
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253 ## log file
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254 ##---------
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255
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256 log_print("Start of the '", modNamC, "' Galaxy module call")
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257
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258 ## arguments
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259 ##----------
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260
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261 args_env <- new.env()
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262
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263 # files
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264
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265 log_print("PARAMETERS (raw):")
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266 invisible(
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267 lapply(
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268 X = 1:length(argVc)
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269 , FUN = function(i) {
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270 log_print(sprintf(" - %s: %s", names(argVc)[i], argVc[i]))
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271 }
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272 )
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273 )
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274
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275 # write.table(as.matrix(argVc), col.names=F, quote=F, sep='\t')
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276
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277 ## output files
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278 sampleMetadata_out <- as.character(argVc["sampleMetadata_out"])
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279 variableMetadata_out <- as.character(argVc["variableMetadata_out"])
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280 scores_out <- as.character(argVc["scores_out"])
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281 ## input files
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282 args_env$data_matrix_path <- as.character(argVc["data_matrix_path"])
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283 args_env$variable_metadata_path <- as.character(argVc["variable_metadata_path"])
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284 args_env$sample_metadata_path <- as.character(argVc["sample_metadata_path"])
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285
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286 # other parameters
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287
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288 # multi-string args - split csv: "1,2,3" -> c("1","2","3")
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289 args_env$kfeatures <- strsplit(x = as.character(argVc['kfeatures']), split = ",", fixed = TRUE)[[1]]
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290 args_env$ksamples <- strsplit(x = as.character(argVc['ksamples' ]), split = ",", fixed = TRUE)[[1]]
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291 # numeric args
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292 args_env$iter_max <- as.numeric( argVc['iter_max' ])
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293 args_env$nstart <- as.numeric( argVc['nstart' ])
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294 args_env$slots <- as.numeric( argVc['slots' ])
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295 # string args
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296 args_env$algorithm <- as.character( argVc['algorithm'])
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297 args_env$log_print <- log_print
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298
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299 log_print("PARAMETERS (parsed):")
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300 for (member in ls(args_env)) {
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301 value <- get(member, args_env)
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302 value <- ifelse(length(value) == 1, value, sprintf("c(%s)", paste(value, collapse=", ")))
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303
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304 log_print(sprintf(" - %s: %s", member, ifelse( !is.function(value) , value, "function" )))
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305 }
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306 log_print("")
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307
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308 ##---------------------------------------------------------
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309 ## Computation - attempt to read input data
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310 ##---------------------------------------------------------
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311 if ( ! read_input_data(args_env, failure_action = read_input_failure_action) ) {
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312 result <- -1
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313 } else {
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314 log_print("Input data was read successfully.")
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315 result <- w4mkmeans(env = args_env)
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316 log_print("returned from call to w4mkmeans.")
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317 }
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318
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319 if ( length(result) == 0 ) {
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320 log_print("no results were produced")
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321 # exit with status code non-zero to indicate error
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322 q(save = "no", status = 1, runLast = FALSE)
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323 } else if ( ! setequal(names(result),c("variableMetadata","sampleMetadata","scores")) ) {
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324 log_print(sprintf("unexpected result keys %s", names(result)))
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325 # exit with status code non-zero to indicate error
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326 q(save = "no", status = 1, runLast = FALSE)
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327 } else if ( ! write_result(result = result$variableMetadata, file_path = variableMetadata_out, kind_string = "clustered variableMetadata")$success ) {
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328 log_print("failed to write output file for clustered variableMetadata")
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329 # exit with status code non-zero to indicate error
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330 q(save = "no", status = 1, runLast = FALSE)
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331 } else if ( ! write_result(result = result$sampleMetadata, file_path = sampleMetadata_out, kind_string = "clustered sampleMetadata")$success ) {
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332 log_print("failed to write output file for clustered sampleMetadata")
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333 # exit with status code non-zero to indicate error
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334 q(save = "no", status = 1, runLast = FALSE)
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335 } else {
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336 tryCatch(
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337 expr = {
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338 fileConn<-file(scores_out)
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339 writeLines(result$scores, fileConn)
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340 close(fileConn)
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341 }
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342 , error = function(e) {
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343 log_print(sprintf("failed to write output file for cluster scores - %s", format_error(e)))
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344 # exit with status code non-zero to indicate error
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345 q(save = "no", status = 1, runLast = FALSE)
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346 }
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347 )
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348 }
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349
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350 ##--------
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351 ## Closing
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352 ##--------
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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353
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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354
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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355 if (!file.exists(sampleMetadata_out)) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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356 log_print(sprintf("ERROR %s::w4m_kmeans_wrapper - file '%s' was not created", modNamC, sampleMetadata_out))
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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357 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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358
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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359 if (!file.exists(variableMetadata_out)) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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360 log_print(sprintf("ERROR %s::w4m_kmeans_wrapper - file '%s' was not created", modNamC, variableMetadata_out))
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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361 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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362
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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363 if (!file.exists(scores_out)) {
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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364 log_print(sprintf("ERROR %s::w4m_kmeans_wrapper - file '%s' was not created", modNamC, scores_out))
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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365 }
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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366
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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367 log_print("Normal termination of '", modNamC, "' Galaxy module call")
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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368
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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369 # exit with status code zero
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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370 q(save = "no", status = 0, runLast = FALSE)