I will post here since I have an issue with one of the GATK3 wrappers that I don't really understand. I want to specify a VCF files with known indels (in the optionnal parameters). But it doesn't work and I have this error :
Traceback (most recent call last):
File "/home/galaxy/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job
File "/home/galaxy/lib/galaxy/jobs/__init__.py", line 862, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/home/galaxy/lib/galaxy/tools/evaluation.py", line 422, in build
NotFound: cannot find 'consensusDeterminationModel' while searching for 'analysis_type.consensusDeterminationModel'
So I looked to the wrapper indel_realigner.xml. From what I see the consensusDeterminationModel is well determined in the macro_optional_parameters with the right values, and then the block analysis_type.optional_parameters.optional_parameters_enabled seems to be OK as well. And there is no spelling errors.
Why this options is not found by the wrapper ? I see nothing that could explain this error :(