I am trying to run GATK's DepthOFCoverage  using intervals and get the following error:

failure preparing job

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job
    job_wrapper.prepare()
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 424, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1827, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1330381526_3_23629.py", line 402, in respond
NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics'

the parameters used are: 

Tool: Depth of Coverage
Name:	Depth of Coverage on data 35 and data 27 (per locus coverage)
Created:	Feb 27, 2012
Filesize:	0 bytes
Dbkey:	human_g1k_v37
Format:	rtable
Tool Version:	None
Tool Standard Output:	stdout
Tool Standard Error:	stderr

Input Parameter	Value
Conditional (reference_source)	0
BAM file	35: Table Recalibration on data 33, data 31, and data 27 (BAM)
Using reference genome	human_g1k_v37
RefSeq Rod	No dataset
Partition type for depth of coverage	sample
Output format	rtable
Conditional (gatk_param_type)	1
How strict should we be in validating the pedigree information	STRICT
Genomic intervals	27: 5um_amplicons_hg19.picard.list
Interval set rule	UNION
Conditional (downsampling_type)	0
Type of BAQ calculation to apply in the engine	OFF
BAQ gap open penalty (Phred Scaled)	40.0
Use the original base quality scores from the OQ tag	False
Value to be used for all base quality scores, when some are missing	-1
How strict should we be with validation	STRICT
Interval merging rule	ALL
Disable experimental low-memory sharding functionality.	False
Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run	False
Conditional (analysis_param_type)	0

I can run this analysis outside of Galaxy with the command: 

java -jar /opt/GenomeAnalysisTK/GenomeAnalysisTK.jar -T DepthOfCoverage -et NO_ET -R /home/galaxy/genome/human_g1k_v37/picard/human_g1k_v37.fasta --partitionType sample --out out.txt --outputFormat rtable -I bamfile.bam --intervals intervals_picardList.list

I'd like to add the DepthOfCoverage to the end of a work flow and get per base coverage for a set of amplicon  coordinates, so using an interval file is needed. 

any suggestions on what is wrong?

*******************************************************

Curtis J. Palm             cpalm@stanford.edu

Stanford Genome Technology Center

MC:  8307

office: 650-812-1994        

*******************************************************

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