In addition to our adhoc testing there is one test, "TestTools", that should be run before each release
and any time you make a major change to the sdk.  TestTools tests the sdk's ability to run all of the released 
tools.  

Source for the test is in: 
	sdk/src/main/java/org/ngbw/examples/TestTools.java.

Properties and data for the test is in: 
	sdk/src/main/resources/examples/tooltest

	In this directory, the files test.properties and testInputFiles.properties have a block for each
	tool that is to be tested.  The block in test.properties gives the values of the non-file parameters for 
	the tool, while testInputFiles.properties gives the values for the parameters that are input files
	for the tool.  For each tool there is also a subdirectory that contains the input files referenced
	by testInputFiles.properties.   The name of the subdirectory is the uppercase name of the tool.

How to Add a Tool:
	You can generate the test.properties and testInputFiles.properties entries for a tool by using
	the code generation in the web project.

		1. Go to web/src/main/codeGeneration

		2. Run "ant clean generate Test"

		3. cd AUTO-GENERATED.

		4. Copy and paste the block for the new tool from test.properties in the AUTO-GENERATED directory
		to test.properties in sdk/src/main/resources/examples/tooltest.  

		5. Repeat for testInputFiles.properties.  You can of course edit the generated parameter blocks to test with different options 
		and/or files. 

		6. Create a subdirectory for the tool in sdk/src/main/resources/examples/tooltest and put a data
		file for the test there. The name of the file must match the name given in testInputFiles.properties.
		Make sure the directory name is all uppercase and that the case of the filename exactly matches what's
		in testInputFiles.properties.

		7. Rebuild the sdk (cd sdk; mvn clean install)

		8. All tools that have (uncommented) entries in test.properties should run successfully.  
		If a developer makes substantial changes to the sdk he'll run the test on all the tools 
		in test.properties and if a tool fails he should assume that he broke something.  So, please 
		don't commit your changes to the properties files unless the test succeeds.  Or comment out 
		your changes before committing.

How to Run the Test:
	From the command line:
		sdk/scripts/sdkrun org.ngbw.examples.TestTools  (tests all tools listed in test.properties)
		sdk/scripts/sdkrun org.ngbw.examples.TestTools PROBALIGN RAXML (tests only probalign and raxml)

	From eclipse: 
		just run the TestTools class in the debugger.  It will test all the tools unless you specify
		specific tools as "Arguments".

	Expected output:
		For each tool that is being tested you should see "TESTING: toolname" followed by many lines of debugging
		output.  Finally you should see a line that includes "COMPLETED : SUCCESS  ... Output files successfully
		retrieved. Task Completed", followed by a list of output files that were retrieved.  This repeats for 
		each tool being tested.

		In general, if a test fails, TestTools exits.  So it's safe to assume that if the last message printed
		looks like the expected output described above the whole group of tools you tested passed.  

	Where to run the test:
		The tools will run wherever they're configured to run in tool-registry.xml in your sdk.  You can 
		test tools that are configured to run on 8ball from your desktop, but tools that are configured to run 
		on the cluster must either be reconfigured to run on 8ball or you'll need to build the sdk on 8ball 
		(or any other machine that's configured as an sge submission host for the cluster) and run the test 
		from the command line on 8ball.

	Note that even if you are only testing one or two tools (by naming them on the command line) all tools
	that have entries in test.properties and testInputFiles.properties will be processed to some extent. 
	They won't be run, but their input files will be loaded so the data files must exist.