Mandatory parameters should allways allow to set no default value in the tool xml

[bernt-matthias]

Describe the bug

Sometimes it's not possible to set a reasonable default for a tool parameter in the tool XML but users must set a value. This is currently not possible at least for numeric parameters and selects.

Numeric parameters produce an error like the following on tool loading.

galaxy.tool_util.toolbox.base ERROR 2023-11-01 21:36:19,551 [pN:main,p:3706683,tN:MainThread] Error reading tool from path: /home/berntm/projects/tools-iuc/tools/hmmer3/hmmsearch.xml
Traceback (most recent call last):
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 865, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 1092, in load_tool
    tool = self.create_tool(
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 530, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 546, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 340, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 802, in __init__
    raise e
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 799, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 1123, in parse
    self.parse_inputs(self.tool_source)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 1414, in parse_inputs
    inputs = self.parse_input_elem(page_source, enctypes)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 1559, in parse_input_elem
    case.inputs = self.parse_input_elem(case_inputs_source, enctypes, context)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 1609, in parse_input_elem
    param = self.parse_param_elem(input_source, enctypes, context)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/__init__.py", line 1622, in parse_param_elem
    param = ToolParameter.build(self, input_source)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 319, in build
    return parameter_types[param_type](tool, input_source)
  File "/tmp/tmpdrabum4r/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 506, in __init__
    raise ParameterValueError("the attribute 'value' must be set for non optional parameters", self.name, None)

Galaxy Version and/or server at which you observed the bug Galaxy Version: 23.1

Expected behavior

value attribute can be omitted for tool definition user should not be able to submit the tool if no value is set.

[nsoranzo]

The workaround is to use value="" in the XML param. It is true though that is a bit annoying and misleading that you cannot leave the attribute out.

[bernt-matthias]

Thanks for the hint. Sounds like this workaround could be implemented in the Galaxy code pretty easily (usually there are horrible side effects when I think like this). What do you think? Maybe a profile version?

[nsoranzo]

I have a patch, working on tests now. No need to have profile changes.

[nsoranzo]

Fixed in #16966 .