--- a/rgToolFactory.py	Thu Mar 20 05:50:38 2014 -0400
+++ b/rgToolFactory.py	Thu Mar 20 05:57:09 2014 -0400
@@ -349,7 +349,7 @@
             else:
                 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
             tooldeps = toolhtmldep % hlp
-            depf = open('tool_dependencies.xml','w')
+            depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
             depf.write(hlp)
             depf.write('\n')
             depf.close()
@@ -363,8 +363,8 @@
                 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
             if self.opts.output_dir:
                 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
-        op = '%s.py' % self.toolname # new name
-        outpiname = os.path.join(tdir,op) # path for the tool tarball
+        outpif = '%s.py' % self.toolname # new name
+        outpiname = os.path.join(tdir,outpif) # path for the tool tarball
         pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
         notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
         notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)