If you type
at the Terminal command line prompt, does it work?
If it works from a Terminal session, then there must be something in your Terminal environment that does not exist when running from Automator. Look at your python script for any environment variables you expect to use and then run add
Run Shell Script
to your Automator script and after running it, use the Terminal to look at /tmp/automator.environment.txt and see if it has the variables you need.
Do you really have the command between "..." in Automator? or did you just do that for your forum posting? If it is inside "..." the sell will not parse it properly.
Can you describe what your script is suppose to do?
In addition to Bob's question about what it's supposed to do, you should state what it does do.
For example, does it give you an error message? do something unexpected? fail silently?
That will go a long way to helping pinpoint the issue.
Additionally, you say:
I know its not recognizing the /applications part of the line.
How do you know this?
Also realize that as far as the shell is concerned, /Applications is not the same as /applications. Case matters.