TnSeq and Whole Genome Sequencing

I have sequenced my transposon libraries, but instead of using transposon insertion sequencing, I sequenced it through whole genome sequencing.

I am new to GALAXY, and I wonder, can I still use the “Essential gene detection with transposon insertion sequencing” workflow? If not, any suggestions on how to approach the massive sequencing data to find the location and frequency of insertion of the transposon into the genome?
Thank you!