fix ms2deepscore lint errors

[hechth]

Linting repository /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore
.. INFO: Included files all found.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No repository_dependencies.xml, skipping.
.. INFO: .shed.yml found and appears to be valid YAML.
.. INFO: No README found, skipping.
.. INFO: No tool_dependencies.xml, skipping.
+Linting tool /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore/ms2deepscore_config_generator.xml
Failed linting
.. WARNING (TestsCaseValidation): Test 1: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [Invalid parameter name found layers_0|dims]
.. CHECK (TestsNoValid): 1 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 18 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [ms2deepscore_config_generator].
.. CHECK (ToolNameValid): Tool defines a name [MS2DeepScore Configuration Generator].
.. CHECK (ToolProfileLegacy): Tool targets 16.01 Galaxy profile.
.. CHECK (ToolVersionValid): Tool defines a version [2.0.0+galaxy0].
.. INFO (CommandInfo): Tool contains a command.
.. CHECK (CitationsFound): Found 2 citations.
.. INFO: Found all shed metadata fields required for automated repository creation and/or updates.
Linting repository /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore
.. INFO: Included files all found.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No repository_dependencies.xml, skipping.
.. INFO: .shed.yml found and appears to be valid YAML.
.. INFO: No README found, skipping.
.. INFO: No tool_dependencies.xml, skipping.
+Linting tool /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore/ms2deepscore_training.xml
.. CHECK (TestsNoValid): 1 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 3 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [ms2deepscore_training].
.. CHECK (ToolNameValid): Tool defines a name [MS2DeepScore Model Training].
.. CHECK (ToolProfileLegacy): Tool targets 16.01 Galaxy profile.
.. CHECK (ToolVersionValid): Tool defines a version [2.0.0+galaxy0].
.. INFO (CommandInfo): Tool contains a command.
.. CHECK (CitationsFound): Found 2 citations.
.. INFO: Found all shed metadata fields required for automated repository creation and/or updates.
Linting repository /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore
.. INFO: Included files all found.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No repository_dependencies.xml, skipping.
.. INFO: .shed.yml found and appears to be valid YAML.
.. INFO: No README found, skipping.
.. INFO: No tool_dependencies.xml, skipping.
+Linting tool /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore/ms2deepscore_similarity.xml
Failed linting
.. WARNING (TestsCaseValidation): Test 1: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [2 validation errors for PydanticModelFor[ms2deepscore_similarity]
scores.__absent__.queries
  Field required [type=missing, input_value={}, input_type=dict]
scores.__absent__.references
  Field required [type=missing, input_value={}, input_type=dict]]
.. WARNING (TestsCaseValidation): Test 2: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [2 validation errors for PydanticModelFor[ms2deepscore_similarity]
scores.__absent__.queries
  Field required [type=missing, input_value={}, input_type=dict]
scores.__absent__.references
  Field required [type=missing, input_value={}, input_type=dict]]
.. CHECK (TestsNoValid): 2 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 6 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [ms2deepscore_similarity].
.. CHECK (ToolNameValid): Tool defines a name [MS2DeepScore Similarity].
.. CHECK (ToolProfileLegacy): Tool targets 16.01 Galaxy profile.
.. CHECK (ToolVersionValid): Tool defines a version [2.0.0+galaxy0].
.. INFO (CommandInfo): Tool contains a command.
.. CHECK (CitationsFound): Found 2 citations.
.. INFO: Found all shed metadata fields required for automated repository creation and/or updates.
Linting repository /home/runner/work/galaxytools/galaxytools/tools/ms2deepscore
.. INFO: Included files all found.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: No repository_dependencies.xml, skipping.
.. INFO: .shed.yml found and appears to be valid YAML.
.. INFO: No README found, skipping.
.. INFO: No tool_dependencies.xml, skipping.
.. INFO: Found all shed metadata fields required for automated repository creation and/or updates.
+ lint_fail=true