Fix for testing extra files in tool tests.

Wouldn't be testing if primary file didn't specify a filename to test against.

lib/galaxy/tools/parameters/output_collect.py

@@ -613,6 +613,7 @@ def collect_primary_datasets(tool, output, tool_provided_metadata, job_working_d
                     extra_files_path_joined = os.path.join(job_working_directory, extra_files_path)
                     for root, dirs, files in os.walk(extra_files_path_joined):
                         extra_dir = os.path.join(primary_data.extra_files_path, root.replace(extra_files_path_joined, '', 1).lstrip(os.path.sep))
+                        extra_dir = os.path.normpath(extra_dir)
                         for f in files:
                             app.object_store.update_from_file(
                                 primary_data.dataset,
@@ -620,7 +621,6 @@ def collect_primary_datasets(tool, output, tool_provided_metadata, job_working_d
                                 alt_name=f,
                                 file_name=os.path.join(root, f),
                                 create=True,
-                                dir_only=True,
                                 preserve_symlinks=True
                             )
             metadata_dict = new_primary_datasets_attributes.get('metadata', None)

lib/galaxy/tools/verify/__init__.py

@@ -69,6 +69,9 @@ def verify(
             errmsg += str(err)
             raise AssertionError(errmsg)
 
+    if attributes is None:
+        attributes = {}
+
     if filename is not None:
         local_name = get_filename(filename)
         temp_name = make_temp_fname(fname=filename)
@@ -88,8 +91,6 @@ def verify(
             else:
                 log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (keep_outputs_dir, ofn))
         try:
-            if attributes is None:
-                attributes = {}
             compare = attributes.get('compare', 'diff')
             if attributes.get('ftype', None) in ['bam', 'qname_sorted.bam', 'qname_input_sorted.bam', 'unsorted.bam']:
                 local_fh, temp_name = _bam_to_sam(local_name, temp_name)
@@ -110,10 +111,6 @@ def verify(
                 files_contains(local_name, temp_name, attributes=attributes)
             else:
                 raise Exception('Unimplemented Compare type: %s' % compare)
-            if verify_extra_files:
-                extra_files = attributes.get('extra_files', None)
-                if extra_files:
-                    verify_extra_files(extra_files)
         except AssertionError as err:
             errmsg = '%s different than expected, difference (using %s):\n' % (item_label, compare)
             errmsg += "( %s v. %s )\n" % (local_name, temp_name)
@@ -123,6 +120,11 @@ def verify(
             if 'GALAXY_TEST_NO_CLEANUP' not in os.environ:
                 os.remove(temp_name)
 
+    if verify_extra_files:
+        extra_files = attributes.get('extra_files', None)
+        if extra_files:
+            verify_extra_files(extra_files)
+
 
 def make_temp_fname(fname=None):
     """Safe temp name - preserve the file extension for tools that interpret it."""