Previously it would copy the collection but not the elements, so if the original HDAs were deleted or purged they'd be deleted in the new history as well. This was not the behavior of the "Copy Datasets" page for instance that would do a deep copy.
There are downsides of doing it this way but this is probably the most intuitive behavior for the GUI for now. Fixes#7493.
The mulled container resolvers are building containers that are
namespaced to "local", so I think it makes a lot of sense to
include local in the defaults. This prevents planemo from
building the same image over and over again when run with
`--biocontainers`.
Fixes
```
Traceback (most recent call last):
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 350, in __prepare_job
job_wrapper.prepare(**prepare_kwds)
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 871, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 451, in build
raise e
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 447, in build
self.__build_command_line()
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 472, in __build_command_line
command_line = fill_template(command, context=param_dict)
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/template.py", line 18, in fill_template
return unicodify(Template(source=template_text, searchList=[context]))
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 1018, in unicodify
msg = "Value '%s' could not be coerced to Unicode" % value
File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1555443583_0915494_96112.py", line 261, in respond
File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 288, in valueFromSearchList
executeCallables=executeCallables)
File "/cvmfs/test.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 231, in _valueForName
if executeCallables and hasattr(nextObj, '__call__') and \
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/wrappers.py", line 138, in __getattr__
self._fields[name] = self._input.options.get_field_by_name_for_value(name, self._value, None, self._other_values)
File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/parameters/dynamic_options.py", line 658, in get_field_by_name_for_value
assert field_name in self.columns, "Requested '%s' column missing from column def" % field_name
AssertionError: Requested '__call__' column missing from column def
```
reported by @natefoo and seen on test.galaxyproject.org.
This was fixed upstream in https://github.com/CheetahTemplate3/cheetah3/commit/354c885ae50c3d38b06928493ecd640c5d3bf768
by replacing `hasattr(nextObj, '__call__')` with `callable(nextObj)`.
Remove copy and paste problems, remote excess configuration unrelated to the what is being tested (handler configuration, multiple worker counts, etc..).
John Chilton