--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_wgcna_render.R	Fri Nov 22 19:45:39 2019 -0500
@@ -0,0 +1,108 @@
+# ------------------------------------------------------------------
+# Set options and load libraries.
+# ------------------------------------------------------------------
+
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE, error=function() {
+          cat(geterrmessage(), file=stderr())
+          quit("no", 1, F)
+})
+
+# We need  to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+options(warn = -1)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(rmarkdown)
+  library(getopt)
+  library(WGCNA)
+  library(caret)
+  library(ggplot2)
+  library(reshape2)
+  # Uncomment for HTML-based reports.
+  #library(DT)  
+  #library(htmltools)
+})
+
+
+# ------------------------------------------------------------------
+# Handle arguments from command line
+# ------------------------------------------------------------------
+
+# Get the tool arguments.
+spec = matrix(c(
+    # Input Files
+    'trait_data',                  't', 2, 'character',
+    'expression_data',             'e', 1, 'character',
+
+    # Input Arguments
+    'missing_value1',              'i', 1, 'character',
+    'missing_value2',              'o', 2, 'character',
+    'sname_col',                   'c', 2, 'integer',
+    'min_cluster_size',            's', 1, 'integer',
+    'height_cut',                  'h', 2, 'double',
+    'power',                       'p', 2, 'double',
+    'block_size',                  'b', 1, 'integer',
+    'hard_threshold',              'j', 1, 'double',
+    'one_hot_cols',                'y', 2, 'character',
+    'ignore_cols',                 'x', 2, 'character',
+
+    # Output Files
+    'gene_module_file',            'k', 1, 'character',
+    'network_edges_file',          'w', 1, 'character',
+    'gene_association_file',       'g', 2, 'character',
+    'module_association_file',     'm', 2, 'character',
+    'module_association_report',   'q', 2, 'character',
+    'network_construction_report', 'r', 1, 'character',
+    'updated_trait_matrix',        'z', 2, 'character',
+    'r_data',                      'a', 1, 'character',
+    'render_log_file',             'l', 1, 'character',
+    'filtered_GEM',                'd', 1, 'character'
+  ),
+  byrow=TRUE, ncol=4)
+
+opt = getopt(spec)
+
+# We have to have values for the one_hot_cols and ignore_cols but the
+# fact these are optional means that we might not get a value for them and the
+# getopt function will then leave them out.  So, we need to make sure they are
+# there.
+if (!"one_hot_cols" %in% names(opt)) {
+  opt[["one_hot_cols"]] <- ''
+}
+if (!"ignore_cols" %in% names(opt)) {
+  opt[["ignore_cols"]] <- ''
+}
+
+# Define environment variables for all input values. This will allow use
+# of the input arguments in the Rmarkdown template file.
+do.call(Sys.setenv, opt[-1])
+
+# ------------------------------------------------------------------
+# Render Rmd files
+# ------------------------------------------------------------------
+tool_directory = Sys.getenv('TOOL_INSTALL_DIR')
+
+
+# We don't want the Rmarkdown STDOUT to show up in Galaxy, so save it to a file.
+zz = file(opt$render_log_file)
+sink(zz)
+sink(zz, type = 'message')
+
+# Print the options
+print(opt)
+
+# Next render the R markdown template file.
+system(command = paste0('cp ', tool_directory, '/aurora_wgcna.Rmd ./'))
+render(input = 'aurora_wgcna.Rmd',  output_file = opt$network_construction_report)
+
+# If the trait data was provided then we'll continue the
+# analysis.
+if (!is.null(opt$trait_data)) {
+  system(command = paste0('cp ', tool_directory, '/aurora_wgcna_trait.Rmd ./'))
+  render(input = 'aurora_wgcna_trait.Rmd',  output_file = opt$module_association_report)
+}
+
+sink()