Mercurial > repos > galaxyp > data_manager_custom

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