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?
Peter
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.