When running bowtie on the command line I was able to use more than one fastq file as input simply by listing them separated by a comma eg:
bowtie -p 3 -q -m 2 --best --strata --sam --chunkmb 256 /databank/indices/bowtie/hg18/hg18 input1.fastq,input2.fastq output.sam
How can I do this within galaxy? The "Map with Bowtie for Illumina" tool only allows for 1 input fastq file as far as I can see.