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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
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2
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3 ################################################################################################
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4 # WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE) #
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5 # #
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6 # Author: Ophelie BARBET #
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7 # User: Galaxy #
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8 # Original data: used with Corr_Script_samples_row.R #
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9 # Starting date: #
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10 # V-1: First version of wrapper #
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11 # #
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12 # #
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13 # Input files: 2 tables with common samples file #
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14 # Output files: Correlation table ; Heatmap file #
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15 # #
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16 ################################################################################################
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17
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18
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19 library(batch) #necessary for parseCommandArgs function
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20 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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21
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22 source_local <- function(...){
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23 argv <- commandArgs(trailingOnly = FALSE)
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24 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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25 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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26 }
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27 #Import the different functions
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28 source_local("Corr_Script_samples_row.R")
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29
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30
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31 if(length(args) < 10){ stop("NOT enough argument !!!") }
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32
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33
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34 cat('\n--------------------------------------------------------------------',
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35 '\nParameters used in "Between-table Correlation":\n\n')
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36 print(args)
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37 cat('--------------------------------------------------------------------\n\n')
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38
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39
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40 risk_alpha <- NULL
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41 correct_multi <- NULL
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42 if(args$test_corr == "yes"){
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43 risk_alpha <- args$risk_alpha
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44 correct_multi <- args$correct_multi
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45 }
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46
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47 filters_choice <- NULL
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48 threshold <- NULL
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49 if(args$filter == "yes"){
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50 filters_choice <- args$filters_choice
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51 if(filters_choice == "filters_0_thr"){
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52 threshold <- args$threshold
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53 }
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54 }
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55
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56 type_classes <- NULL
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57 reg_class_value <- NULL
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58 irreg_class_vect <- NULL
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59 if(args$color_heatmap == "yes"){
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60 type_classes <- args$type_classes
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61 if(type_classes == "regular"){
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62 reg_class_value <- args$reg_class_value
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63 } else if(type_classes == "irregular"){
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64 irreg_class_vect <- eval(parse(text=paste0("c",args$irreg_class_vect)))
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65 }
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66 }
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67
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68
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69 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$filter, filters_choice, threshold,
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70 args$reorder_var, args$color_heatmap, type_classes, reg_class_value, irreg_class_vect, args$tabcorr_out, args$heatmap_out)
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71
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72
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73 cat('\n--------------------------------------------------------------------',
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74 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
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75 sessionInfo()
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76 cat('--------------------------------------------------------------------\n\n')
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77
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78
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79 #delete the parameters to avoid the passage to the next tool in .RData image
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80 rm(args) |
