3.2 years ago by
The most commonly used tool for this sort of analysis that I know of is LEfSe. This is tools is available in the Tool Shed for use in a local or cloud Galaxy. A search by "GO" in the Tool Shed will bring up other options to review. See the 3rd party documentation for each tool to review usage details. Most Galaxy wrappers incorporate at least the major parameters for common usage.
Also, if you used a reference GTF dataset with the analysis, then the attribute gene_name assigned to the output can be used with several tools in the group "Phenotype Association". If you need to map gene names or symbols but you have the wrong ones in your output (to match the target tool), the "xref" table associated with several genomes from UCSC can be helpful in converting terms. Obtain this table from the UCSC Table Browser. The idea would be to join the list of terms you have with that table to link in another source's terms, then use those new terms as input as a link to GO. This is a bit more tedious to do, but is an option.
Hopefully this helps, Jen, Galaxy team