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

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/customProDB_annotation.R	Fri Jan 15 15:52:56 2016 -0500
@@ -0,0 +1,69 @@
+#!/usr/bin/env Rscript
+
+initial.options <- commandArgs(trailingOnly = FALSE)
+script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+## 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$dbkey <- make_option('--dbkey', type='character')
+option_list$outputFile <- make_option('--outputFile', type='character')
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+
+customProDB_annotation <- function(
+	dbkey = GalaxyCharacterParam(required=TRUE), 
+	outputFile = GalaxyOutput("output","json"))
+{
+    if (file.exists(outputFile))
+    {
+        if (file.info(outputFile)$size > 0) { gstop("output file already exists") }
+        else
+        {
+            tryCatch(
+            {
+                file.remove(outputFile)
+            }, error=function(err)
+            {
+                gstop("failed to remove empty existing file")
+            })
+        }
+    }
+
+    gstop("what you talkin bout willis?!")
+}
+
+
+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(customProDB_annotation, params)
+
+## end warning handler
+}, warning = function(w) {
+    cat(paste("Warning:", conditionMessage(w), "\n"))
+    invokeRestart("muffleWarning")
+})