Allow tool tests to assert properties about command, standard output, and standard error.

See test/functional/tools/job_properties.xml for example. Provides full access to assertion based XML tags - tabular and XML based assertions probably not so interesting so these include - has_text, has_line, not_has_text, has_text_matching, has_line_matching.

test/functional/test_toolbox.py

@@ -1,6 +1,7 @@
 import new
 import sys
 from base.twilltestcase import TwillTestCase
+from base.asserts import verify_assertions
 from base.interactor import build_interactor, stage_data_in_history, RunToolException
 from base.instrument import register_job_data
 from galaxy.tools import DataManagerTool
@@ -132,6 +133,21 @@ class ToolTestCase( TwillTestCase ):
         if job_stdio is None:
             job_stdio = galaxy_interactor.get_job_stdio( jobs[0][ 'id' ] )
 
+        other_checks = {
+            "command_line": "Command produced by the job",
+            "stdout": "Standard output of the job",
+            "stderr": "Standard error of the job",
+        }
+        for what, description in other_checks.items():
+            if getattr( testdef, what, None ) is not None:
+                try:
+                    data = job_stdio[what]
+                    verify_assertions( data, getattr( testdef, what ) )
+                except AssertionError, err:
+                    errmsg = '%s different than expected\n' % description
+                    errmsg += str( err )
+                    found_exceptions.append( AssertionError( errmsg ) )
+
         if found_exceptions:
             raise JobOutputsError(found_exceptions, job_stdio)
         else: