Mercurial > repos > melpetera > generic_filter
diff GalFilter/filter_wrap.R @ 3:cfd7c4aa5c26 draft default tip
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author | melpetera |
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date | Fri, 03 Jan 2020 04:09:28 -0500 |
parents | 2c9afaf849ad |
children |
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--- a/GalFilter/filter_wrap.R Tue Jun 27 05:57:04 2017 -0400 +++ b/GalFilter/filter_wrap.R Fri Jan 03 04:09:28 2020 -0500 @@ -10,6 +10,7 @@ # 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 # # # # # # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt # @@ -19,6 +20,23 @@ library(batch) #necessary for parseCommandArgs function + +# 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 = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects source_local <- function(...){ @@ -32,6 +50,14 @@ 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") ){ @@ -59,5 +85,13 @@ # 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)