since your are migrating to autosys from some native tool, then first of all you have to make it clear and understand the mindset that none of the tool can do the same thing in exact manner as it was done by others.
Business requirements / Scenarios have to be tweaked or modified as per the new tool and al these have to be modified as per tool fitments.
Coming to the question, can you please explain or elaborate more to get more clarity on scenario. From the post as per I can think of, there is a file which gets generated at the agent side and that file sets or have the value and based on that value, the script is getting executed . am I right?
if yes, then questions:
1. how the file is getting generated? is it automatic or manual?
2. how the value of the variable is set? is it automatic / script or manual?
3. based on variable's value, specific script is being run - is that hard coded in the script?
From autosys perspective, since the autosys agent has already being installed on these agents, so you can use a file trigger job to watch for a specific naming convention file, then you can read the file for a specific text (file read job) then you can trigger the specific script as command job.
file trigger -> File read -> Command Job
However, it is quite possible that you wont be able to met the same functionality as native tool without modifying or tweaking the script / business.
Also, files handling (deletion of old files / creation of old files etc) have to be handled or take in to consideration.