Mercurial > repos > bcclaywell > microbiome_community_suite
view getAttributeList.R @ 0:12b4f093e6c4 draft default tip
planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author | bcclaywell |
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date | Mon, 12 Oct 2015 16:46:15 -0400 |
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#!/usr/bin/env Rscript ## begin warning handler withCallingHandlers({ library(methods) # Because Rscript does not always do this options('useFancyQuotes' = FALSE) suppressPackageStartupMessages(library("optparse")) suppressPackageStartupMessages(library("RGalaxy")) option_list <- list() option_list$CommunityFile <- make_option('--CommunityFile', type='character') option_list$OutputFile <- make_option('--OutputFile', type='character') opt <- parse_args(OptionParser(option_list=option_list)) suppressPackageStartupMessages(library(microbiomePkg)) ## function body not needed here, it is in package params <- list() for(param in names(opt)) { if (!param == "help") params[param] <- opt[param] } setClass("GalaxyRemoteError", contains="character") wrappedFunction <- function(f) { tryCatch(do.call(f, params), error=function(e) new("GalaxyRemoteError", conditionMessage(e))) } suppressPackageStartupMessages(library(RGalaxy)) do.call(getAttributeList, params) ## end warning handler }, warning = function(w) { cat(paste("Warning:", conditionMessage(w), "\n")) invokeRestart("muffleWarning") })