Danielle,
> When using Export to File, it appears that galaxy renames each output
> file to something generic datXXX.dat and changes the filename
> extension (to .dat). How do I convince Galaxy to preserve my
> filenames so I know which file is which ?
There is currently no way to do this but it would definitely be a useful option
to have. I've opened a ticket that you can follow and/or comment on if you're
interested:
https://bitbucket.org/galaxy/galaxy-central/issue/680/preserve-dataset-names-when-exporting
> Is there some other way to download multiple output files and preserve
> their names and file extensions?
Not currently, but this is on wish list and will likely get done at some point
in the future.
J.
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