filter_wrap.R

#!/usr/bin/Rscript --vanilla --slave --no-site-file

################################################################################################
# WRAPPER FOR filter_script.R (GENERIC FILTERS)                                                #
#                                                                                              #
# Author: Melanie PETERA based on Marion LANDI's filters' wrapper                              #
# User: Galaxy                                                                                 #
# Original data: used with filter_script.R                                                     #
# Starting date: 04-09-2014                                                                    #
# V-1: Restriction of old filter wrapper to Filter according to factors                        #
# V-1.1: Modification to allow the choice of meta-data table for filtering                     #
# V-2: Addition of numerical filter                                                            #
# V-2.5: -h option + additional information in stdout                                          #
# V-2.6: The tool does not rely on the batch package anymore to parse its command line.        #                                                                                #
#                                                                                              #
# Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                      #
# Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt                     #
#                                                                                              #
################################################################################################


parse_args <- function() {
  args <- commandArgs()
  start <- which(args == "--args")[1] + 1
  if (is.na(start)) {
    return(list())
  }
  seq_by2 <- seq(start, length(args), by = 2)
  result <- as.list(args[seq_by2 + 1])
  names(result) <- args[seq_by2]
  return(result)
}

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

# Help
if (length(grep('-h', argv)) >0) {
	cat("Usage:", prog.name,
      "dataMatrix_in myDataMatrix.tsv",
      "sampleMetadata_in mySampleMetadata.tsv",
      "variableMetadata_in myVariableMetadata.tsv",
      "...",
		"\n")
	quit(status = 0)
}

args <- parse_args() #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("filter_script.R","RcheckLibrary.R","miniTools.R")


if(length(args) < 8){ stop("NOT enough argument !!!") }


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


list_num <- NULL
if(!is.null(args$parm_col)){
	for( i in which(names(args)=="num_file") ){
		if(args[[i+2]] %in% c("lower","upper")){
		  list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]])))
		}
		if(args[[i+2]] %in% c("between","extremity")){
		  list_num <- c(list_num, list(c(args[[i]], args[[i+1]], args[[i+2]],args[[i+3]],args[[i+4]])))
		}
	}
}	

list_fact <- NULL
if(!is.null(args$factor_col)){
	for( i in which(names(args)=="qual_file") ){
		list_fact <- c(list_fact, list(c(args[[i+1]], args[[i+2]], args[[i]])))
	}
}	

filters(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in,
        args$Numeric, list_num, args$Factors, list_fact,
        args$dataMatrix_out, args$sampleMetadata_out, args$variableMetadata_out)

#filters(ion.file.in, meta.samp.file.in, meta.ion.file.in,
#        NUM, ls.num, FACT, ls.fact,
#        ion.file.out, meta.samp.file.out, meta.ion.file.out)


cat('\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"))


#delete the parameters to avoid the passage to the next tool in .RData image
rm(args)