To include After Effects scripting in a command line (Windows only):

Following are examples of DOS shell scripts that will send an existing .jsx file containing an After Effects script to the application without using the After Effects user interface to execute the script.

In the first example, you would copy and paste your After Effects script directly into the command line script and then run it, as follows (your script text would appear in quotes following the afterfx.exe -s command):

afterfx.exe -s "alert ("You just sent an alert to After Effects")"

Alternatively, you could specify the location of the .jsx file to be executed, as follows:

afterfx.exe -r c:\myDocuments\Scripts\yourAEScriptHere.jsx

Furthermore, two other options, "-sq" and "-rq" perform the same functions as "-s" and "-r" respectively, but additionally prevent any dialogs or other user interaction from being displayed while the script is running.

afterfx.exe -sq "alert ("You just sent an alert to After Effects")"
afterfx.exe -rq c:\myDocuments\Scripts\yourAEScriptHere.jsx