[24.0] Raise appropriate exception if accessing deleted input file

[mvdbeek]

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[galaxyproject-sentryintegration]

Sentry Issue: GALAXY-MAIN-Q6N