[galaxy-user] Mapping to only 3 genes / targeted resequencing / SOLiD4 / short reads

Hi! Following situation: 10 barcoded "samples". Each sample consists of a mix of the sequences 3 independent genes (á 2 alleles). I would like to map the SOLiD4 reads only to the sequences of those 3 genes, patient by patient. First, the 10 barcoded samples have to be separated from each other. Then, the short reads have to be mapped to the sequences of the 3 genes, which are available in FASTA-format (single) or multi-FASTA-format (all sequences in one file). Is this possible using the available GALAXY tools? How? Thank you in advance. Jose