Update denoise_wrapper.py

Fixed filepaths-problem when using multiple flowgram-files in the commandline. 
Lines 47,99-113
Update denoise_wrapper.py

Sorry for editing so late. I am pretty much noobish in this github-game :-). I just tried this code on some samples and it worked well. Hopefully it workes for you, too. Have a nice weekend all together.
Merge pull request #896 from paulomat/patch-1

Update denoise_wrapper.py