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>