[galaxy-dev] barcode splitter made 96 files. Is there a tool to map all of these files to the reference genome?

Hi, I have Rad tag data that I'm trying to map to our reference genome in Galaxy on our local instance. After barcode splitter, I have 96 files (one each of all of the sequences for that individual). It seems like the current tools (e.g. bowtie) can only map a single file to the reference. I think that even if I were to do this step 96 times, I would still end up with 96 files at the end and not the linkage map that I hoped for. Any ideas on how to move forward from this stage? -Lucinda