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
')
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