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
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