# HG changeset patch
# User galaxyp
# Date 1452891176 18000
# Node ID 3c2c36beddb1ef69ca90b72768aae2b7b79fcfc9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
diff -r 000000000000 -r 3c2c36beddb1 data_manager/customProDB_annotation.R
--- /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)$size > 0) { gstop("output file already exists") }
+ else
+ {
+ tryCatch(
+ {
+ file.remove(outputFile)
+ }, error=function(err)
+ {
+ gstop("failed to remove empty existing file")
+ })
+ }
+ }
+
+ gstop("what you talkin bout willis?!")
+}
+
+
+params <- list()
+for(param in names(opt))
+{
+ if (!param == "help")
+ params[param] <- opt[param]
+}
+
+setClass("GalaxyRemoteError", contains="character")
+wrappedFunction <- function(f)
+{
+ tryCatch(do.call(f, params),
+ error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
+}
+
+
+suppressPackageStartupMessages(library(RGalaxy))
+do.call(customProDB_annotation, params)
+
+## end warning handler
+}, warning = function(w) {
+ cat(paste("Warning:", conditionMessage(w), "\n"))
+ invokeRestart("muffleWarning")
+})
diff -r 000000000000 -r 3c2c36beddb1 data_manager/customProDB_annotation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/customProDB_annotation.xml Fri Jan 15 15:52:56 2016 -0500
@@ -0,0 +1,31 @@
+
+ builder
+ customProDB_annotation.R
+ --outputFile "${out_file}"
+ --dbkey "${dbkey}"
+ 2>&1
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+
+
diff -r 000000000000 -r 3c2c36beddb1 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Jan 15 15:52:56 2016 -0500
@@ -0,0 +1,22 @@
+
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+