Mercurial > repos > melpetera > corr_table
view CorrTable/Corr_wrap.r @ 0:b22c453e4cf4 draft
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author | melpetera |
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date | Thu, 11 Oct 2018 05:35:55 -0400 |
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children | 29ec7e3afdd4 |
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#!/usr/bin/Rscript --vanilla --slave --no-site-file ################################################################################################ # WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE) # # # # Author: Ophelie BARBET # # User: Galaxy # # Original data: used with Corr_Script_samples_row.R # # Starting date: # # V-1: First version of wrapper # # # # # # Input files: 2 tables with common samples file # # Output files: Correlation table ; Heatmap file # # # ################################################################################################ library(batch) #necessary for parseCommandArgs function args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects source_local <- function(...){ argv <- commandArgs(trailingOnly = FALSE) base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))} } #Import the different functions source_local("Corr_Script_samples_row.R") if(length(args) < 10){ stop("NOT enough argument !!!") } cat('\n--------------------------------------------------------------------', '\nParameters used in "Between-table Correlation":\n\n') print(args) cat('--------------------------------------------------------------------\n\n') risk_alpha <- NULL correct_multi <- NULL if(args$test_corr == "yes"){ risk_alpha <- args$risk_alpha correct_multi <- args$correct_multi } filters_choice <- NULL threshold <- NULL if(args$filter == "yes"){ filters_choice <- args$filters_choice if(filters_choice == "filters_0_thr"){ threshold <- args$threshold } } type_classes <- NULL reg_class_value <- NULL irreg_class_vect <- NULL if(args$color_heatmap == "yes"){ type_classes <- args$type_classes if(type_classes == "regular"){ reg_class_value <- args$reg_class_value } else if(type_classes == "irregular"){ irreg_class_vect <- eval(parse(text=paste0("c",args$irreg_class_vect))) } } correlation.tab(args$tab1_in, args$tab2_in, args$tab1_samples, args$tab2_samples, args$corr_method, args$test_corr, risk_alpha, correct_multi, args$filter, filters_choice, threshold, args$reorder_var, args$color_heatmap, type_classes, reg_class_value, irreg_class_vect, args$tabcorr_out, args$heatmap_out) cat('\n--------------------------------------------------------------------', '\nInformation about R (version, Operating System, attached or loaded packages):\n\n') sessionInfo() cat('--------------------------------------------------------------------\n\n') #delete the parameters to avoid the passage to the next tool in .RData image rm(args)