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Explicitly cast BamTools Filter's rules param to a string #1922

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merged 1 commit into from Jun 5, 2018

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@natefoo natefoo commented Jun 5, 2018

Fixes the job setup error encountered when a rule is defined:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job
    job_wrapper.prepare()
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 865, in prepare
    self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build
    raise e
TypeError: <galaxy.tools.wrappers.InputValueWrapper object at 0x7f2929ada2d0> is not JSON serializable

I am not sure if this worked in some older version of Galaxy and failed due to tool framework changes, but this fixes it for 18.05, at least.

Originally reported in galaxyproject/usegalaxy-playbook#116.

@nsoranzo nsoranzo merged commit 36169ce into galaxyproject:master Jun 5, 2018
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