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1 #!/usr/bin/env Rscript
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2
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3 ################################################################################################
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4 # batch_correction_wrapper #
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5 # #
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6 # Authors: Marion LANDI / Jean-Francois MARTIN / Melanie Petera #
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7 # User: Galaxy #
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8 # Original data: -- #
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9 # Starting date: 22-07-2014 #
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10 # Version 1: 22-07-2014 #
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11 # Version 2: 08-12-2014 #
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12 # Version 2.1: 09-01-2015 modification in Error message of sample matching #
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13 # Version 2.2: 16-03-2015 inclusion of miniTools' functions for special characters #
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14 # Version 2.90: 18-08-2015 new parameter valnull #
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15 # Version 2.91: 25-08-2016 error message improvment #
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16 # Version 3: 02-10-2020 #
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17 # - split of tool-linked code and script-linked one #
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18 # - addition of args print and sessionInfo() #
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19 # - adjustment of sample tags' parameters to 3L methods #
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20 # - addition of the min.norm argument in meth3L() call #
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21 # #
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22 # Input files: dataMatrix.txt, sampleMetadata.txt, variableMetadata.txt (BC only) #
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23 # Output files: graph.pdf, corrected table (BC only), diagnostic table (DBC only), #
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24 # variableMetadata (BC only) #
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25 # #
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26 ################################################################################################
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27
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28
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29 library(batch) #necessary for parseCommandArgs function
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30
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31 ##------------------------------
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32 ## test help option
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33 ##------------------------------
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34
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35 # Prog. constants
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36 argv.help <- commandArgs(trailingOnly = FALSE)
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37 script.path <- sub("--file=", "", argv.help[grep("--file=", argv.help)])
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38 prog.name <- basename(script.path)
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39
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40 # Test Help
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41 if (length(grep('-h', argv.help)) > 0) {
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42 cat("Usage: Rscript ",
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43 prog.name,
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44 "{args} \n",
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45 "parameters: \n",
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46 "\tanalyse {val}: must be set to \"batch_correction\"",
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47 "\tdataMatrix {file}: set the input data matrix file (mandatory) \n",
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48 "\tsampleMetadata {file}: set the input sample metadata file (mandatory) \n",
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49 "\tvariableMetadata {file}: set the input variable metadata file (mandatory) \n",
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50 "\tmethod {opt}: set the method; can set to \"linear\", \"lowess\" or \"loess\" (mandatory) \n",
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51 "\tspan {condition}: set the span condition; set to \"none\" if method is set to \"linear\" (mandatory) \n",
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52 "\tref_factor {value}: set the ref_factor value; (if span value is set to NULL, optional) \n",
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53 "\tdetail {value}: set the detail value; (if span value is set to NULL, optional) \n",
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54 "\tdataMatrix_out {file}: set the output data matrix file (mandatory) \n",
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55 "\tvariableMetadata_out {file}: set the output variable metadata file (mandatory) \n",
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56 "\tgraph_output {file}: set the output graph file (mandatory) \n",
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57 "\trdata_output {file}: set the output Rdata file (mandatory) \n",
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58 "\tbatch_col_name {val}: the column name for batch. Default value is \"batch\".\n",
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59 "\tinjection_order_col_name {val}: the column name for the injection order. Default value is \"injectionOrder\".\n",
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60 "\tsample_type_col_name {val}: the column name for the sample types. Default value is \"sampleType\".\n",
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61 "\tsample_type_tags {val}: the tags used inside the sample type column, defined as key/value pairs separated by commas (example: blank=blank,pool=pool,sample=sample).\n",
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62 "\n")
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63 quit(status = 0)
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64 }
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65
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66 ##------------------------------
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67 ## init. params
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68 ##------------------------------
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69
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70 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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71
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72
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73 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
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74 '\n\n--------------------------------------------------------------------',
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75 '\nParameters used:\n\n')
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76 print(args)
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77 cat('--------------------------------------------------------------------\n\n')
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78
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79
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80 # Set default col names
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81 if ( ! 'batch_col_name' %in% names(args))
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82 args[['batch_col_name']] <- 'batch'
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83 if ( ! 'injection_order_col_name' %in% names(args))
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84 args[['injection_order_col_name']] <- 'injectionOrder'
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85 if ( ! 'sample_type_col_name' %in% names(args))
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86 args[['sample_type_col_name']] <- 'sampleType'
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87 if ( ! 'sample_type_tags' %in% names(args))
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88 args[['sample_type_tags']] <- 'blank=blank,pool=pool,sample=sample'
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89
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90 # Parse sample type tags
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91 sample.type.tags <- list()
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92 for (kv in strsplit(strsplit(args$sample_type_tags, ',')[[1]], '='))
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93 sample.type.tags[[kv[[1]]]] <- kv[-1]
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94 if ( ! all(c('pool', 'blank', 'sample') %in% names(sample.type.tags)))
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95 stop("All tags pool, blank and sample must be defined in option sampleTypeTags.")
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96 args$sample_type_tags <- sample.type.tags
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97
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98 ##------------------------------
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99 ## init. functions
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100 ##------------------------------
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101
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102 source_local <- function(...){
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103 argv <- commandArgs(trailingOnly = FALSE)
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104 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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105 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
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106 }
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107 #Import the different functions
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108 source_local("batch_correction_3Lfct.R","batch_correction_3Llauncher.R","easyrlibrary-lib/RcheckLibrary.R","easyrlibrary-lib/miniTools.R")
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109
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110 # Specificities of BC and DBC
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111 if(args$analyse == "batch_correction") {
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112 args$out_graph_pdf <- NULL
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113 args$out_preNormSummary <- NULL
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114 }else{
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115 args$variableMetadata <- NULL
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116 args$rdata_output <- NULL
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117 args$dataMatrix_out <- NULL
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118 args$variableMetadata_out <- NULL
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119 args$graph_output <- NULL
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120 args$method <- NULL
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121 args$detail <- NULL
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122 args$valnull <- NULL
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123 }
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124
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125 # Launch tool
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126 meth3L(idsample=args$sampleMetadata, iddata=args$dataMatrix, sample_type_col_name=args$sample_type_col_name, injection_order_col_name=args$injection_order_col_name,
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127 batch_col_name=args$batch_col_name, sample_type_tags=args$sample_type_tags, factbio=args$ref_factor, analyse=args$analyse, metaion=args$variableMetadata,
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128 detail=args$detail, method=args$method, outlog=args$graph_output, span=args$span, valnull=args$valnull, rdata_output=args$rdata_output,
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129 dataMatrix_out=args$dataMatrix_out, variableMetadata_out=args$variableMetadata_out, out_graph_pdf=args$out_graph_pdf, out_preNormSummary=args$out_preNormSummary,
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130 min.norm=1)
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131
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132
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133 cat('\n\n--------------------------------------------------------------------',
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134 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
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135 sessionInfo()
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136 cat('--------------------------------------------------------------------\n',
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137 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
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138
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139 rm(args)
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