Hi, I've been tweaking the GATK wrappers to try to get my pipeline working in Galaxy; for drop-down menus, I've been able to add additional eligible formats to some parameters:
<param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
This works just fine, but it doesn't work for others:
<param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
When I make the change, and reload the configuration (or even restart Galaxy), the menu still doesn't show any options, even though I have a bed file loaded in my history (the same bed file WILL show up in the first menu). Does anyone have an idea what might be wrong?
Thanks, Alex Bigelow