Mercurial > repos > eschen42 > w4mclassfilter
view w4mclassfilter_wrapper.R @ 4:499c7ecfa834 draft
planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
author | eschen42 |
---|---|
date | Mon, 19 Jun 2017 23:42:33 -0400 |
parents | 23c6d271def9 |
children | 38ccf6722d54 |
line wrap: on
line source
#!/usr/bin/env Rscript library(batch) ## parseCommandArgs ######## # MAIN # ######## argVc <- unlist(parseCommandArgs(evaluate=FALSE)) ##------------------------------ ## Initializing ##------------------------------ ## options ##-------- strAsFacL <- options()$stringsAsFactors options(stringsAsFactors = FALSE) ## libraries ##---------- suppressMessages(library(w4mclassfilter)) if(packageVersion("w4mclassfilter") < "0.98.0") stop("Please use 'w4mclassfilter' versions of 0.98.0 and above") ## constants ##---------- modNamC <- "w4mclassfilter" ## module name topEnvC <- environment() flgC <- "\n" ## functions ##---------- flgF <- function(tesC, envC = topEnvC, txtC = NA) { ## management of warning and error messages tesL <- eval(parse(text = tesC), envir = envC) if(!tesL) { #sink(NULL) stpTxtC <- ifelse(is.na(txtC), paste0(tesC, " is FALSE"), txtC) stop(stpTxtC, call. = FALSE) } } ## flgF ## log file ##--------- my_print <- function(x, ...) { cat(c(x, ...))} my_print("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="") ## arguments ##---------- # files dataMatrix_in <- as.character(argVc["dataMatrix_in"]) dataMatrix_out <- as.character(argVc["dataMatrix_out"]) sampleMetadata_in <- as.character(argVc["sampleMetadata_in"]) sampleMetadata_out <- as.character(argVc["sampleMetadata_out"]) variableMetadata_in <- as.character(argVc["variableMetadata_in"]) variableMetadata_out <- as.character(argVc["variableMetadata_out"]) # other parameters sampleclassNames <- as.character(argVc["sampleclassNames"]) wildcards <- as.logical(argVc["wildcards"]) sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]] if (wildcards) { sampleclassNames <- gsub("[.]", "[.]", sampleclassNames) sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE) } inclusive <- as.logical(argVc["inclusive"]) classnameColumn <- as.character(argVc["classnameColumn"]) samplenameColumn <- as.character(argVc["samplenameColumn"]) ##------------------------------ ## Computation ##------------------------------ result <- w4m_filter_by_sample_class( dataMatrix_in = dataMatrix_in , sampleMetadata_in = sampleMetadata_in , variableMetadata_in = variableMetadata_in , dataMatrix_out = dataMatrix_out , sampleMetadata_out = sampleMetadata_out , variableMetadata_out = variableMetadata_out , classes = sampleclassNames , include = inclusive , class_column = classnameColumn , samplename_column = samplenameColumn , failure_action = my_print ) my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ", as.character(result), "\n", sep = "") ##-------- ## Closing ##-------- my_print("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "") #sink() if (!file.exists(dataMatrix_out)) { print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out)) }# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) } if (!file.exists(variableMetadata_out)) { print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out)) } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) } if (!file.exists(sampleMetadata_out)) { print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out)) } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) } if( !result ) { stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC)) } rm(list = ls())