You can use inline asp tags only in asp files. So if you have such tags in your JS you will need to rewrite in such a way that not to use them, and only then you will be able to place the code inside external file.
I see several options for doing that:
1. Use global variables in the JS of your asp page that to holds the value calculated by the inline tags. And then later use these variables in the external js file.
2. Do not use these tags at all. Use events of the controls and store the "sender" into some variables when needed.
3. Use directly the ID of the controls when you know them and they are not dynamically set.
You can write us some examples in which you use these tags, and we could try to point you some workarounds for the exact cases.
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