changeset 0:8a7ee199a315 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/R_test.R	Tue Oct 28 06:25:06 2014 -0400
@@ -0,0 +1,16 @@
+systemUser <- system("whoami",T)
+rVersion <- R.version.string
+
+cat( "Starting R_test\n" )	
+cat( rVersion, "\n" )
+cat( systemUser, "\n" )
+
+#qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
+
+packs <- c()
+for ( pack in packs ){
+	catMsg( c("Loading ", pack) )
+	library( pack )
+}
+
+q(status=0)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/R_test.xml	Tue Oct 28 06:25:06 2014 -0400
@@ -0,0 +1,45 @@
+<tool id="R_test" name="R_test" version="1" force_history_refresh="True">
+  
+  <requirements>
+    <requirement type="package" version="3.1.0">R</requirement>
+  </requirements>
+
+  <description>Package to test R package install</description>
+
+  <command interpreter="Rscript"> 
+    R_test.R 
+  </command>
+
+  <stdio>
+    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
+    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
+    <exit_code range="1:" level="fatal" description="R script didnt finish correctly, check log" />
+  </stdio>
+  
+  <inputs>
+    
+    <!-- Job name: must contain non-whitespace chars -->
+    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
+      <validator type="empty_field" />
+      <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
+    </param>
+
+  </inputs>
+
+  <outputs>
+
+    <!-- main output is a html report -->
+    <!-- ...but there can be more outputs using the id of the htmlFile output -->
+    <data format="html" name="htmlFile" label="rTest: ${jobName}" />
+
+  </outputs>
+
+  <help>
+.. class:: infomark
+
+**Introduction**
+
+This is just a tiny package to test R install
+  </help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 28 06:25:06 2014 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+    <package name="R" version="3.1.0">
+        <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    
+</tool_dependency>