Hi Dan,
That's embarrassing - turns out I was editing the wrong XML file! That explains 
it.
(I was working on it remotely, and I guess I didn't notice that I had lost the 
connection - my text editor only saved my changes locally)

Thanks again for your help,
Alex

On Oct 20, 2011, at 9:33 AM, Daniel Blankenberg wrote:

Hi Alex,

The xml file you have attached has the "input_intervals" parameter set to 
accept only gatk_intervals. If I swap it for the parameter that you listed 
below (<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" />), then it works just fine and 
will list bed files. Can you verify that the copy of the xml that you are 
loading for the tool that you are looking at actually has bed specified in the 
format list?


Thanks for using Galaxy,

Dan


On Oct 19, 2011, at 11:01 AM, Alex R Bigelow wrote:

Thanks Dan,
That's comforting that the GATK tools will be updated - I'm guessing that 
you're already properly fixing what I was hacking. I guess I can wait for the 
updated version, so it's no biggie if we fix my specific code - but I think 
there's a chance the problems I was having might be an indicator of a deeper 
bug in Galaxy (or it's perfectly possible that I just messed up).

Here is the whole .xml file - I was in the middle of hacking it, so I know the 
ROD command line bits I messed with are incomplete. I don't think that would be 
relevant, though, to the input intervals menu not showing the bed file as an 
option:

Thanks again,
Alex






On Oct 18, 2011, at 1:46 PM, Daniel Blankenberg wrote:

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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<realigner_target_creator.xml>


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