I'd like to pass the name or dbkey of a reference genome (e.g. hg19) to a tool .
How can I set up a variable to pass to my tool without asking the user to specify the refernece again (i.e. infer the reference from the bam file) ?
I have a BAM file in the tool xml
<param name='bam_file' type='data' optional='false' format='bam' label="Aligned reads (bam)" />
I want to call the tool like this: