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2
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1 # ------------------------------------------------------------------
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2 # Set options and load libraries.
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3 # ------------------------------------------------------------------
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4
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5 # setup R error handline to go to stderr
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6 options(show.error.messages=FALSE, error=function() {
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7 cat(geterrmessage(), file=stderr())
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8 quit("no", 1, F)
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9 })
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10
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11 # We need to not crash galaxy with an UTF8 error on German LC settings.
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12 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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13
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14 options(warn = -1)
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15 args = commandArgs(trailingOnly=TRUE)
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16
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17 suppressPackageStartupMessages({
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14
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18 library(rmarkdown)
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2
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19 library(getopt)
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20 library(WGCNA)
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14
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21 library(caret)
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22 library(ggplot2)
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23 library(reshape2)
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24 # Uncomment for HTML-based reports.
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25 #library(DT)
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26 #library(htmltools)
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2
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27 })
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28
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29
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30 # ------------------------------------------------------------------
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31 # Handle arguments from command line
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32 # ------------------------------------------------------------------
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33
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34 # Get the tool arguments.
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35 spec = matrix(c(
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36 # Input Files
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37 'trait_data', 't', 2, 'character',
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38 'expression_data', 'e', 1, 'character',
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6
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39
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2
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40 # Input Arguments
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14
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41 'missing_value1', 'i', 1, 'character',
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42 'missing_value2', 'o', 2, 'character',
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2
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43 'sname_col', 'c', 2, 'integer',
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44 'min_cluster_size', 's', 1, 'integer',
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45 'height_cut', 'h', 2, 'double',
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46 'power', 'p', 2, 'double',
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47 'block_size', 'b', 1, 'integer',
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6
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48 'hard_threshold', 'j', 1, 'double',
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49 'one_hot_cols', 'y', 2, 'character',
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50 'ignore_cols', 'x', 2, 'character',
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51
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2
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52 # Output Files
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53 'gene_module_file', 'k', 1, 'character',
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54 'network_edges_file', 'w', 1, 'character',
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55 'gene_association_file', 'g', 2, 'character',
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56 'module_association_file', 'm', 2, 'character',
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57 'module_association_report', 'q', 2, 'character',
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58 'network_construction_report', 'r', 1, 'character',
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14
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59 'updated_trait_matrix', 'z', 2, 'character',
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2
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60 'r_data', 'a', 1, 'character',
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14
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61 'render_log_file', 'l', 1, 'character',
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62 'filtered_GEM', 'd', 1, 'character'
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2
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63 ),
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64 byrow=TRUE, ncol=4)
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65
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66 opt = getopt(spec)
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67
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6
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68 # We have to have values for the one_hot_cols and ignore_cols but the
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69 # fact these are optional means that we might not get a value for them and the
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70 # getopt function will then leave them out. So, we need to make sure they are
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71 # there.
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72 if (!"one_hot_cols" %in% names(opt)) {
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73 opt[["one_hot_cols"]] <- ''
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74 }
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75 if (!"ignore_cols" %in% names(opt)) {
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76 opt[["ignore_cols"]] <- ''
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77 }
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78
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2
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79 # Define environment variables for all input values. This will allow use
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80 # of the input arguments in the Rmarkdown template file.
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81 do.call(Sys.setenv, opt[-1])
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82
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83 # ------------------------------------------------------------------
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84 # Render Rmd files
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85 # ------------------------------------------------------------------
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86 tool_directory = Sys.getenv('TOOL_INSTALL_DIR')
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87
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88
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89 # We don't want the Rmarkdown STDOUT to show up in Galaxy, so save it to a file.
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90 zz = file(opt$render_log_file)
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91 sink(zz)
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92 sink(zz, type = 'message')
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93
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6
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94 # Print the options
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95 print(opt)
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96
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2
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97 # Next render the R markdown template file.
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98 system(command = paste0('cp ', tool_directory, '/aurora_wgcna.Rmd ./'))
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99 render(input = 'aurora_wgcna.Rmd', output_file = opt$network_construction_report)
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100
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6
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101 # If the trait data was provided then we'll continue the
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2
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102 # analysis.
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103 if (!is.null(opt$trait_data)) {
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104 system(command = paste0('cp ', tool_directory, '/aurora_wgcna_trait.Rmd ./'))
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105 render(input = 'aurora_wgcna_trait.Rmd', output_file = opt$module_association_report)
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106 }
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107
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108 sink()
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