Mercurial > repos > galaxyp > data_manager_custom

comparison data_manager/customProDB_annotation.R @ 0:3c2c36beddb1 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 15 Jan 2016 15:52:56 -0500
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-1:000000000000 0:3c2c36beddb1
1 #!/usr/bin/env Rscript
2
3 initial.options <- commandArgs(trailingOnly = FALSE)
4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
5
6 ## begin warning handler
7 withCallingHandlers({
8
9 library(methods) # Because Rscript does not always do this
10
11 options('useFancyQuotes' = FALSE)
12
13 suppressPackageStartupMessages(library("optparse"))
14 suppressPackageStartupMessages(library("RGalaxy"))
15
16
17 option_list <- list()
18 option_list$dbkey <- make_option('--dbkey', type='character')
19 option_list$outputFile <- make_option('--outputFile', type='character')
20
21 opt <- parse_args(OptionParser(option_list=option_list))
22
23
24 customProDB_annotation <- function(
25 dbkey = GalaxyCharacterParam(required=TRUE),
26 outputFile = GalaxyOutput("output","json"))
27 {
28 if (file.exists(outputFile))
29 {
30 if (file.info(outputFile)$size > 0) { gstop("output file already exists") }
31 else
32 {
33 tryCatch(
34 {
35 file.remove(outputFile)
36 }, error=function(err)
37 {
38 gstop("failed to remove empty existing file")
39 })
40 }
41 }
42
43 gstop("what you talkin bout willis?!")
44 }
45
46
47 params <- list()
48 for(param in names(opt))
49 {
50 if (!param == "help")
51 params[param] <- opt[param]
52 }
53
54 setClass("GalaxyRemoteError", contains="character")
55 wrappedFunction <- function(f)
56 {
57 tryCatch(do.call(f, params),
58 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
59 }
60
61
62 suppressPackageStartupMessages(library(RGalaxy))
63 do.call(customProDB_annotation, params)
64
65 ## end warning handler
66 }, warning = function(w) {
67 cat(paste("Warning:", conditionMessage(w), "\n"))
68 invokeRestart("muffleWarning")
69 })