Mercurial > repos > spficklin > aurora_wgcna
view aurora_wgcna_render.R @ 5:75b87f1278a2 draft
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author | spficklin |
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date | Thu, 21 Nov 2019 09:26:00 +0000 |
parents | d947c300617c |
children | 083886b3f3db |
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# ------------------------------------------------------------------ # 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") # suppress warning options(warn = -1) options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) args = commandArgs(trailingOnly=TRUE) suppressPackageStartupMessages({ library(getopt) library(tools) library(WGCNA) }) # Load libraries library(rmarkdown) library(WGCNA) library(DT) library(htmltools) library(ggplot2) # ------------------------------------------------------------------ # 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_value', 'i', 1, '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, 'integer', # 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', 'r_data', 'a', 1, 'character', 'render_log_file', 'l', 1, 'character' ), byrow=TRUE, ncol=4) opt = getopt(spec) # 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$render_log_file) sink(zz) sink(zz, type = 'message') # Next render the R markdown template file. system(command = paste0('cp ', tool_directory, '/aurora_wgcna.Rmd ./')) render(input = 'aurora_wgcna.Rmd', output_file = opt$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()