def test_03_input(instance_path):
"""Check the essential input parameters."""
whale = Path(instance_path) / 'whale.txt'
whale.touch()
argv = [
'echo',
'-f',
'-i42',
'--example-string',
'hello',
'--file=whale.txt',
]
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
assert tool.arguments[0].prefix == '-f'
assert tool.inputs[0].default == 42
assert tool.inputs[0].type == 'int'
assert tool.inputs[0].inputBinding.prefix == '-i'
assert tool.inputs[0].inputBinding.separate is False
assert tool.inputs[1].default == 'hello'
assert tool.inputs[1].type == 'string'
assert tool.inputs[1].inputBinding.prefix == '--example-string'
assert tool.inputs[1].inputBinding.separate is True
assert tool.inputs[2].default.path == Path('whale.txt')
assert tool.inputs[2].type == 'File'
assert tool.inputs[2].inputBinding.prefix == '--file='
assert tool.inputs[2].inputBinding.separate is False
assert tool.to_argv() == argv
def test_09_array_inputs(instance_path):
"""Test specification of input parameters in arrays."""
argv = [
'echo',
'-A',
'one',
'two',
'three',
'-B=four',
'-B=five',
'-B=six',
'-C=seven,eight,nine',
]
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
# TODO add grouping for -A and -B
assert tool.inputs[-1].type == 'string[]'
assert tool.inputs[-1].default == ['seven', 'eight', 'nine']
assert tool.inputs[-1].inputBinding.prefix == '-C='
assert tool.inputs[-1].inputBinding.itemSeparator == ','
assert tool.inputs[-1].inputBinding.separate is False
assert tool.to_argv() == argv
def test_short_base_command_detection():
"""Test base command detection without arguments."""
tool = CommandLineToolFactory(('echo', 'A')).generate_tool()
assert tool.cwlVersion == 'v1.0'
assert tool.__class__.__name__ == 'CommandLineTool'
assert tool.inputs[0].default == 'A'
assert tool.to_argv() == ['echo', 'A']
def test_base_command_detection(instance_path):
"""Test base command detection."""
hello = Path(instance_path) / 'hello.tar'
hello.touch()
argv = ['tar', 'xf', 'hello.tar']
tool = CommandLineToolFactory(argv,
directory=instance_path).generate_tool()
assert tool.baseCommand == ['tar', 'xf']
assert tool.inputs[0].default.path == Path('hello.tar')
assert tool.inputs[0].type == 'File'
assert tool.inputs[0].inputBinding.prefix is None
assert tool.inputs[0].inputBinding.separate is True
assert tool.to_argv() == argv