I have a java web application that needs to make use of a python script. The web application will give the script a file as input and take some text as output. 
I have two options:

Wrap the python script with HTTP and call it from the web application as a REST service
Simply execute command line from the web application

Which option should I take and why? This script won't be used by any other application.
I would personally recommend wrapping the Python code in an HTTP layer and turning it into a REST web service. I don't doubt that many successful applications have been written by calling scripts from the command line, but I think there are a couple things that are really nice when it comes to the freedoms of a web service. It definitely seems like putting the Python app in a web service would be the more 'Service-oriented' way to do it, so it seems reasonable to expect that doing so would give you the typical benefits of SOA.
This may or may not apply to your situation, but if none of these considerations apply that seems to point towards this being a 'neither choice will be that bad' situation.
The biggest thing I see going for using the web service is scalability. If the command line application can chew up a lot of server resources, it would be good to have it running on a separate server from the web application. That way, other users who aren't using the part of the application that interacts with this Python app won't have their experience reduced when other users do things that cause the Python app to be called. Putting the Python code behind a web service would also make it easier to cluster. If it's a situation where you could get some benefit from caching, it would also be easy to take advantage of the caching mechanisms in HTTP and your proxy servers.
Another thing that might be nice is testability. There's a lot of good tools out there for testing the common cases of a web application talking to a web service, whereas thoroughly testing your applications when they're just calling command line applications might be a little more work.
Execute the script in command line or in Rest client