Thanks for clarifying, I thought this ^^ was what you had sequenced.
WGS reads can be mapped with Bowtie2 or BWA/BWA-MEM or BLASTN against a reference genome. Success involves doing some QA/QC on the reads, setting the correct parameters for the mapping tool used, and (possibly, if a built-in index is not available) making sure the custom reference genome is formatted correctly.
See the tool forms for abbreviated help and links to the full documentation. Parameters available on Galaxy tool forms are for the most part the same as when using the tools line command.
Many of the Galaxy tutorials include QA/QC and mapping steps. Help for Custom Genome formatting is here. Also please see: Troubleshooting resources for errors or unexpected results