changeset 3:3d7aaffea9f8 default tip

commit test2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/addTwoNumbers.R	Wed Nov 19 13:14:01 2014 +0900
@@ -0,0 +1,56 @@
+#!/usr/bin/env Rscript
+
+## 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$number1 <- make_option('--number1', type='numeric')
+option_list$number2 <- make_option('--number2', type='numeric')
+option_list$sum <- make_option('--sum', type='character')
+
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+suppressPackageStartupMessages(library(RSclient))
+
+## function body not needed here, it is in package
+
+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)))
+}
+
+
+c <- RS.connect(host='localhost', port=6311)
+RS.eval(c, options('useFancyQuotes' = FALSE))
+RS.eval(c, suppressPackageStartupMessages(library(RGalaxy)))
+RS.assign(c, 'params', params)
+RS.assign(c, 'wrappedFunction', wrappedFunction)
+RS.eval(c, setClass('GalaxyRemoteError', contains='character'))
+res <- RS.eval(c, wrappedFunction(addTwoNumbers))
+RS.close(c)
+if(is(res, 'GalaxyRemoteError'))RGalaxy::gstop(res)
+
+## end warning handler
+}, warning = function(w) {
+    cat(paste("Warning:", conditionMessage(w), "\n"))
+    invokeRestart("muffleWarning")
+})

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/addTwoNumbers.xml	Wed Nov 19 13:14:01 2014 +0900
@@ -0,0 +1,32 @@
+<tool id="addTwoNumbers" name="Add Two Numbers" version="1.10.0">
+  <description>Add two numbers</description>
+  <command interpreter="Rscript --vanilla">addTwoNumbers.R
+       #if str($number1).strip() != "":
+          --number1="$number1"
+       #end if
+       #if str($number2).strip() != "":
+          --number2="$number2"
+       #end if
+       #if str($sum).strip() != "":
+          --sum="$sum"
+       #end if
+
+2&gt;&amp;1</command>
+  <inputs>
+    <param optional="false" name="number1" type="float" value="" help="The first number to add." label="[required] Number1">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param optional="false" name="number2" type="float" value="" help="The second number to add." label="[required] Number2">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="sum" label="sum.txt"/>
+  </outputs>
+  <help>
+**Description**
+
+An example function that can be made into a Galaxy tool.  Takes
+two numbers, adds them, and returns a file containing the result.
+</help>
+</tool>
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