Mercurial > repos > bcclaywell > microbiome_community_suite

comparison community.R @ 0:12b4f093e6c4 draft default tip

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planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
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-1:000000000000 0:12b4f093e6c4
1 #!/usr/bin/env Rscript
2
3 ## begin warning handler
4 withCallingHandlers({
5
6 library(methods) # Because Rscript does not always do this
7
8 options('useFancyQuotes' = FALSE)
9
10 suppressPackageStartupMessages(library("optparse"))
11 suppressPackageStartupMessages(library("RGalaxy"))
12
13
14 option_list <- list()
15
16 option_list$CountsFile <- make_option('--CountsFile', type='character')
17 option_list$SamplesFile <- make_option('--SamplesFile', type='character')
18 option_list$K <- make_option('--K', type='numeric')
19 option_list$A <- make_option('--A', type='numeric')
20 option_list$Transform <- make_option('--Transform', type='character')
21 option_list$SampleName <- make_option('--SampleName', type='character')
22 option_list$ColumnClasses <- make_option('--ColumnClasses', type='character')
23 option_list$OutputFile <- make_option('--OutputFile', type='character')
24
25
26 opt <- parse_args(OptionParser(option_list=option_list))
27
28 suppressPackageStartupMessages(library(microbiomePkg))
29
30 ## function body not needed here, it is in package
31
32 params <- list()
33 for(param in names(opt))
34 {
35 if (!param == "help")
36 params[param] <- opt[param]
37 }
38
39 setClass("GalaxyRemoteError", contains="character")
40 wrappedFunction <- function(f)
41 {
42 tryCatch(do.call(f, params),
43 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
44 }
45
46
47 suppressPackageStartupMessages(library(RGalaxy))
48 do.call(community, params)
49
50 ## end warning handler
51 }, warning = function(w) {
52 cat(paste("Warning:", conditionMessage(w), "\n"))
53 invokeRestart("muffleWarning")
54 })