--- a/toolfactory/rgToolFactory2.py	Tue Nov 10 03:24:28 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Tue Nov 10 23:53:32 2020 +0000
@@ -843,7 +843,6 @@
             p = subprocess.run(
                     cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy,
                 )
-            dummy.close() # throw all the log away as it will be rerun after outputs are generated
         else:
             cll = ["planemo", "test", "--galaxy_root",
                 self.args.galaxy_root,
@@ -927,6 +926,8 @@
                 dest = os.path.join(self.repdir, ofn)
                 src = os.path.join(self.tooloutdir, entry.name)
                 shutil.copyfile(src, dest)
+                if entry.name.startswith('tool_test_output'):
+                    os.unlink(src)
 
 
 def main():