annotate BC/batch_correction_3Lwrapper.R @ 4:23314e1192d4 draft default tip

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#!/usr/bin/env Rscript

################################################################################################
# batch_correction_wrapper                                                                     #
#                                                                                              #
# Authors: Marion LANDI / Jean-Francois MARTIN / Melanie Petera                                #
# User: Galaxy                                                                                 #
# Original data: --                                                                            #
# Starting date: 22-07-2014                                                                    #
# Version 1: 22-07-2014                                                                        #
# Version 2: 08-12-2014                                                                        #
# Version 2.1: 09-01-2015 modification in Error message of sample matching                     #
# Version 2.2: 16-03-2015 inclusion of miniTools' functions for special characters             #
# Version 2.90: 18-08-2015 new parameter valnull                                               #
# Version 2.91: 25-08-2016 error message improvment                                            #
# Version 3: 02-10-2020                                                                        #
#            - split of tool-linked code and script-linked one                                 #
#            - addition of args print and sessionInfo()                                        #
#            - adjustment of sample tags' parameters to 3L methods                             #
#            - addition of the min.norm argument in meth3L() call                              #
#                                                                                              #
# Input files: dataMatrix.txt, sampleMetadata.txt, variableMetadata.txt (BC only)              #
# Output files: graph.pdf, corrected table (BC only), diagnostic table (DBC only),             #
#               variableMetadata (BC only)                                                     #
#                                                                                              #
################################################################################################


library(batch) #necessary for parseCommandArgs function

##------------------------------
## test help option
##------------------------------

# Prog. constants
argv.help <- commandArgs(trailingOnly = FALSE)
script.path <- sub("--file=", "", argv.help[grep("--file=", argv.help)])
prog.name <- basename(script.path)

# Test Help
if (length(grep('-h', argv.help)) > 0) {
  cat("Usage: Rscript ", 
    prog.name,
    "{args} \n",
    "parameters: \n",
    "\tanalyse {val}: must be set to \"batch_correction\"",
    "\tdataMatrix {file}: set the input data matrix file (mandatory) \n",
    "\tsampleMetadata {file}: set the input sample metadata file (mandatory) \n",
    "\tvariableMetadata {file}: set the input variable metadata file (mandatory) \n",
    "\tmethod {opt}: set the method; can set to \"linear\", \"lowess\" or \"loess\" (mandatory) \n",
    "\tspan {condition}: set the span condition; set to \"none\" if method is set to \"linear\" (mandatory) \n", 
    "\tref_factor {value}: set the ref_factor value; (if span value is set to NULL, optional) \n",
    "\tdetail {value}: set the detail value; (if span value is set to NULL, optional) \n",
    "\tdataMatrix_out {file}: set the output data matrix file (mandatory) \n",
    "\tvariableMetadata_out {file}: set the output variable metadata file (mandatory) \n",
    "\tgraph_output {file}: set the output graph file (mandatory) \n",
    "\trdata_output {file}: set the output Rdata file (mandatory) \n",
    "\tbatch_col_name {val}: the column name for batch. Default value is \"batch\".\n",
    "\tinjection_order_col_name {val}: the column name for the injection order. Default value is \"injectionOrder\".\n",
    "\tsample_type_col_name {val}: the column name for the sample types. Default value is \"sampleType\".\n",
    "\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",
    "\n")
  quit(status = 0)
}

##------------------------------
## init. params
##------------------------------

args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects


cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
'\n\n--------------------------------------------------------------------', 
'\nParameters used:\n\n')
print(args)
cat('--------------------------------------------------------------------\n\n')


# Set default col names
if ( ! 'batch_col_name' %in% names(args))
    args[['batch_col_name']] <- 'batch'
if ( ! 'injection_order_col_name' %in% names(args))
    args[['injection_order_col_name']] <- 'injectionOrder'
if ( ! 'sample_type_col_name' %in% names(args))
    args[['sample_type_col_name']] <- 'sampleType'
if ( ! 'sample_type_tags' %in% names(args))
    args[['sample_type_tags']] <- 'blank=blank,pool=pool,sample=sample'

# Parse sample type tags
sample.type.tags <- list()
for (kv in strsplit(strsplit(args$sample_type_tags, ',')[[1]], '='))
    sample.type.tags[[kv[[1]]]] <- kv[-1]
if ( ! all(c('pool', 'blank', 'sample') %in% names(sample.type.tags)))
    stop("All tags pool, blank and sample must be defined in option sampleTypeTags.")
args$sample_type_tags <- sample.type.tags

##------------------------------
## init. functions
##------------------------------

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("batch_correction_3Lfct.R","batch_correction_3Llauncher.R","easyrlibrary-lib/RcheckLibrary.R","easyrlibrary-lib/miniTools.R")

# Specificities of BC and DBC
if(args$analyse == "batch_correction") {
  args$out_graph_pdf <- NULL
  args$out_preNormSummary <- NULL
}else{
  args$variableMetadata <- NULL
  args$rdata_output <- NULL
  args$dataMatrix_out <- NULL
  args$variableMetadata_out <- NULL
  args$graph_output <- NULL
  args$method <- NULL
  args$detail <- NULL
  args$valnull <- NULL
}

# Launch tool
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,
       batch_col_name=args$batch_col_name, sample_type_tags=args$sample_type_tags, factbio=args$ref_factor, analyse=args$analyse, metaion=args$variableMetadata,
       detail=args$detail, method=args$method, outlog=args$graph_output, span=args$span, valnull=args$valnull, rdata_output=args$rdata_output,
       dataMatrix_out=args$dataMatrix_out, variableMetadata_out=args$variableMetadata_out, out_graph_pdf=args$out_graph_pdf, out_preNormSummary=args$out_preNormSummary,
       min.norm=1)


cat('\n\n--------------------------------------------------------------------',
'\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
sessionInfo()
cat('--------------------------------------------------------------------\n',
'\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))

rm(args)