Hi Peter, I ending up finding a solution to my problem using this forum post: https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html. I just ended up using the really specific file output path and it started auto-detecting the file format. Thanks for your help it was much appreciated.

On Thu, Jun 30, 2016 at 1:01 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Maybe sharing your tool XML file would be best - is it on GitHub?


On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu
<katherine.beaulieu014@gmail.com> wrote:
> Ok, so I don't give the user the option to select the correct data type to
> reduce the amount of stuff the user has to know when using the tool.
> I do leave the format as auto and Galaxy just leaves it as the generic data
> type 'data'.
> As for how the format is defined in Galaxy, I'm not quite sure what the
> answer to this question is because I am just testing the tool with really
> simple text files, with extension .txt. and it can't seem to pick it up, it
> just leaves it as 'data'. Also not quite sure how to test the Python code in
> the sniff function outside of Galaxy... (only starting working with Galaxy 3
> weeks ago).
> Let me know if I should provide you with the tool config file if that would
> be a little more useful. It's quite straightforward
> Thanks for helping with this.