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galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry
Apache License 2.0
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new tool for computing RMSD, using gmx #156

Closed thepineapplepirate closed 1 year ago

blankenberg commented 2 years ago

I can reproduce test failures when running with biocontainers Docker, looks to be due to differences in rounding/precision: planemo test --biocontainers tools/gromacs/rmsd.xml

FAIL: ( gmx_rmsd ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/test/functional/test_toolbox.py", line 98, in test_tool
    self.do_it(tool_version=tool_version, test_index=test_index)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/test/functional/test_toolbox.py", line 35, in do_it
    verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1127, in verify_tool
    raise e
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1123, in verify_tool
    job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1299, in _verify_outputs
    raise JobOutputsError(found_exceptions, job_stdio)
galaxy.tool_util.verify.interactor.JobOutputsError: Output rmsdmirror_output:  different than expected
Expected text '0.3000000    0.1366720' in output ('   0.0000000    0.1520911
   0.1000000    0.1420089
   0.2000000    0.1430562
   0.3000000    0.1366719
   0.4000000    0.1393728
   0.5000000    0.1362066
   0.6000000    0.1527199
   0.7000000    0.1565393
   0.8000000    0.1589817
   0.9000000    0.1475553
   1.0000000    0.1428274
')
Output rmsd_output:  different than expected
Expected text '0.1000000    0.0208356' in output ('   0.0000000    0.0016154
   0.1000000    0.0208355
   0.2000000    0.0297601
   0.3000000    0.0322985
   0.4000000    0.0262557
   0.5000000    0.0309702
   0.6000000    0.0231878
   0.7000000    0.0207828
   0.8000000    0.0175181
   0.9000000    0.0170825
   1.0000000    0.0250765
')
-------------------- >> begin captured stdout << ---------------------
FAIL: ( gmx_rmsd ) > Test-2
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/test/functional/test_toolbox.py", line 98, in test_tool
    self.do_it(tool_version=tool_version, test_index=test_index)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/test/functional/test_toolbox.py", line 35, in do_it
    verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1127, in verify_tool
    raise e
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1123, in verify_tool
    job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
  File "/private/var/folders/ml/yp9yj0_d66v7szw8jmtgjnlrkgts7t/T/tmpp2nj597a/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1299, in _verify_outputs
    raise JobOutputsError(found_exceptions, job_stdio)
galaxy.tool_util.verify.interactor.JobOutputsError: Output rmsd_output:  different than expected
Expected text '0.1000000    0.0208356' in output ('   0.0000000    0.0016154
   0.1000000    0.0208355
   0.2000000    0.0297601
   0.3000000    0.0322985
   0.4000000    0.0262557
   0.5000000    0.0309702
   0.6000000    0.0231878
   0.7000000    0.0207828
   0.8000000    0.0175181
   0.9000000    0.0170825
   1.0000000    0.0250765
')