I'm not sure what you're asking.
The Add button in the slic3r GUI allows you to import an STL file.
If you want to slice from the command line, you can specify the stl file on the command line. Here is the template command line I use in my host program:
command = /home/jeff/Slic3r/bin/slic3r --load "%config%" "%stl%" -o "%slicegcode%"
Note that you will need to include a config file. Slic3r from the command line just uses default settings - NOT the settings you last left it with.