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 > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/
realigner_target_creator.xml
Description: realigner_target_creator.xml
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