Hi Alex,
There will be an update to the GATK tools in Galaxy in the coming weeks, for compatibility with version 1.2 of the GATK. There have been several changes that are not directly backwards compatible, including much of the ROD handling (which now will only accept vcf files for the most part) -- just a warning.
However, nothing pops out as looking wrong here, can you share the entire xml and I'll take a look?
Thanks for using Galaxy,
Dan
On Oct 17, 2011, at 7:36 PM, Alex R Bigelow wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: