> 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

I forgot to mention that you can inspect the datasets_attrs.txt to see the 
mapping between datasets and files. datasets_attrs.txt contains a JSON dict, so 
it would be possible to write a little script that renames datasets based on 
the values in the dict.

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