Fixes
```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['bamtools --help'] == ['bamtools --help', 'samtools --help']
Right contains one more item: 'samtools --help'
Full diff:
- ['bamtools --help', 'samtools --help']
+ ['bamtools --help']
```
(again). The test broke with the addition of
`osx-64/samtools-1.3.1-h0840685_11.tar.bz2` 4 days ago.
by extracting all specified files in ``get_files_from_conda_package()``
and processing them in order of precedence.
Fix broken mulled unit test:
```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['bamtools --help'] == ['bamtools --help', 'samtools --help']
Right contains one more item: 'samtools --help'
Full diff:
- ['bamtools --help', 'samtools --help']
+ ['bamtools --help']
```
which failed because, after a new build of samtools 1.3.1 was released,
``get_file_from_conda_package()`` started returning the content of
``info/recipe/meta.yaml.template`` instead of ``info/recipe/meta.yaml``
when called inside ``get_test_from_anaconda()``. Then parsing
the content of ``info/recipe/meta.yaml.template`` in
``get_commands_from_yaml()`` failed with
```
jinja2.exceptions.UndefinedError: 'compiler' is undefined
```
because that file contains ``{{ compiler('c') }}`` .
Broken in https://github.com/galaxyproject/galaxy/pull/15682 .
Fixes:
```
KeyError: 'chrom'
File "galaxy/tools/__init__.py", line 1909, in handle_single_execution
rval = self.execute(
File "galaxy/tools/__init__.py", line 2005, in execute
return self.tool_action.execute(
File "galaxy/tools/actions/__init__.py", line 392, in execute
) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
File "galaxy/tools/actions/__init__.py", line 327, in _collect_inputs
inp_data, all_permissions = self._collect_input_datasets(
File "galaxy/tools/actions/__init__.py", line 268, in _collect_input_datasets
tool.visit_inputs(param_values, visitor)
File "galaxy/tools/__init__.py", line 1748, in visit_inputs
visit_input_values(self.inputs, values, callback)
File "galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
callback_helper(
File "galaxy/tools/parameters/__init__.py", line 159, in callback_helper
new_value = callback(**args)
File "galaxy/tools/actions/__init__.py", line 191, in visitor
input_datasets[prefix + input.name] = process_dataset(value)
File "galaxy/tools/actions/__init__.py", line 126, in process_dataset
data = data.get_converted_dataset(trans, target_ext, target_context=parent, history=history)
File "galaxy/model/__init__.py", line 4211, in get_converted_dataset
self.datatype.convert_dataset(
File "galaxy/datatypes/data.py", line 795, in convert_dataset
job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
File "galaxy/tools/__init__.py", line 2005, in execute
return self.tool_action.execute(
File "galaxy/tools/actions/__init__.py", line 453, in execute
params=wrapped_params.params,
File "galaxy/tools/parameters/wrapped.py", line 43, in params
self.wrap_values(self.tool.inputs, params, skip_missing_values=not self.tool.check_values)
File "galaxy/tools/parameters/wrapped.py", line 58, in wrap_values
value = input_values[input.name]
```
in https://sentry.galaxyproject.org/share/issue/4f2171798f214f7ba8b947eaaebe2776/
Marius van den Beek