Dynamic options will opnly prepend GALAXY_INDEX_DATA_DIR if from_file is not an absolute path. Also fixed a type in twill code.

lib/galaxy/tools/parameters/dynamic_options.py

@@ -152,7 +152,7 @@ class DynamicOptions( object ):
                     filters[ 'params' ][ n ] = v
         if self.data_file and self.data_file.startswith( 'static' ):
             self.data_file_path = self.data_file
-        elif self.data_file not in [ None, 'data_ref' ]:
+        elif self.data_file not in [ None, 'data_ref' ] and not os.path.isabs( self.data_file ):
             self.data_file_path = "%s/%s" % ( trans.app.config.tool_data_path, self.data_file )
         # Now that we've parsed our filters, we need to see if the tool is a maf tool 
         # which requires special handling

test/base/twilltestcase.py

@@ -47,7 +47,7 @@ class TwillTestCase( unittest.TestCase ):
             if files_differ:
                 diff = difflib.unified_diff( local_file, history_data, "local_file", "history_data" )
                 diff_slice = list( islice( diff, 40 ) )
-                if file1.endswith( '.pdf' ) or file2.endswith( 'pdf' ):
+                if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ):
                     # PDF files contain both a creation and modification date, so we need to
                     # handle these differences.  As long as the rest of the PDF file does not differ,
                     # we're ok.