Goseq with custom gene-go-category term inputs = bad scientific outputs

[jennaj]

toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0

That way of using the tool does not actually work for people. The tool needs the full "database" to perform the processing. This seems to be true with the command-line version of the tool, too, so not a "galaxy specific" thing, just how it works.

If the custom file is provided, the statistics and outputs both suffer. This is confusing for users. I am not sure if this ever worked, so I think we should remove that custom option from even being possible on the tool form since what is the intended use?

If I am just missing something, super happy to be corrected! Maybe some situations will work, some won't, and we can clarify that in the tool form help better? I thought I asked about this already but maybe never actually made the ticket. Please merge into the right place as needed. :) Thanks!

Example recent topics at the forum

1. August 2024 https://help.galaxyproject.org/t/goseq-na-na-na-na-values/13248/13?u=jennaj
2. October 2024 (today) https://help.galaxyproject.org/t/trouble-with-goseq/13787/2