Enhancement: allow BiG-SCAPE to process inputs without a required .gbk extension in dataset filename

[jennaj]

The tool interprets the input filename not just the database assignments. Requires a .gbk extension.

There isn't a way to batch rename dataset filenames. Upstreams tools can modify the original input filenames when creating outputs. Currently, users need to manually rename the files (pencil icon) for them to be processed by BiG-SCAPE.

Test history with tool test data adjusted to show the usage issue
https://usegalaxy.eu/u/jenj/h/test-bigscape

stderr is a bit difficult to interpret, and the (optional) extra logs result in failed jobs with no content

No aligned sequences found in the domain folder (run without the --skip_ma parameter or point to the correct output folder)

Reported at https://help.galaxyproject.org/t/renaming-files-in-a-collection/12511