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planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
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12b4f093e6c4 planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
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1 #!/usr/bin/env Rscript
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2
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3 ## begin warning handler
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4 withCallingHandlers({
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5
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6 library(methods) # Because Rscript does not always do this
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8 options('useFancyQuotes' = FALSE)
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9
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10 suppressPackageStartupMessages(library("optparse"))
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11 suppressPackageStartupMessages(library("RGalaxy"))
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12
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14 option_list <- list()
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16 option_list$CountsFile <- make_option('--CountsFile', type='character')
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17 option_list$SamplesFile <- make_option('--SamplesFile', type='character')
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18 option_list$K <- make_option('--K', type='numeric')
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19 option_list$A <- make_option('--A', type='numeric')
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20 option_list$Transform <- make_option('--Transform', type='character')
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21 option_list$SampleName <- make_option('--SampleName', type='character')
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22 option_list$ColumnClasses <- make_option('--ColumnClasses', type='character')
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23 option_list$OutputFile <- make_option('--OutputFile', type='character')
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26 opt <- parse_args(OptionParser(option_list=option_list))
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28 suppressPackageStartupMessages(library(microbiomePkg))
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29
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30 ## function body not needed here, it is in package
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31
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32 params <- list()
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33 for(param in names(opt))
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34 {
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35 if (!param == "help")
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36 params[param] <- opt[param]
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37 }
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39 setClass("GalaxyRemoteError", contains="character")
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40 wrappedFunction <- function(f)
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41 {
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42 tryCatch(do.call(f, params),
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43 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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44 }
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47 suppressPackageStartupMessages(library(RGalaxy))
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48 do.call(community, params)
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49
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50 ## end warning handler
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51 }, warning = function(w) {
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52 cat(paste("Warning:", conditionMessage(w), "\n"))
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53 invokeRestart("muffleWarning")
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54 })