Mercurial > repos > melpetera > batchcorrection
diff BC/batch_correction_3Lwrapper.R @ 4:23314e1192d4 draft default tip
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| author | melpetera |
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| date | Thu, 14 Jan 2021 09:56:58 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BC/batch_correction_3Lwrapper.R Thu Jan 14 09:56:58 2021 +0000 @@ -0,0 +1,139 @@ +#!/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)