Add tool_instance_name parameter to enable multiple TOPP tool configurations

[Copilot]

Calling input_TOPP("IDFilter") multiple times caused widget key collisions in Streamlit session state, preventing the same tool from being used with different parameter configurations in a workflow.

Changes

• StreamlitUI.input_TOPP(): Added optional tool_instance_name parameter

  • Generates unique widget keys using instance name instead of tool name
  • Displays instance identifier in UI (e.g., "IDFilter (IDFilter-strict)")
  • Stores _tool_name metadata for tool resolution

• ParameterManager: Instance-aware parameter handling

  • _get_tool_name_from_instance(): Resolves actual tool name from instance or metadata
  • save_parameters(): Handles instance-specific parameter storage
  • get_topp_parameters(): Retrieves parameters by instance name

• CommandExecutor.run_topp(): Added optional tool_instance_name parameter

  • Uses instance name for parameter lookup
  • Filters out metadata keys (prefix _) from command arguments

Usage

# Configure two instances with different thresholds
self.ui.input_TOPP("IDFilter", 
                   tool_instance_name="IDFilter-strict",
                   custom_defaults={"score:pep": 0.01})

self.ui.input_TOPP("IDFilter", 
                   tool_instance_name="IDFilter-lenient",
                   custom_defaults={"score:pep": 0.05})

# Execute with instance-specific parameters
self.executor.run_topp("IDFilter", {"in": files1, "out": out1}, 
                      tool_instance_name="IDFilter-strict")

self.executor.run_topp("IDFilter", {"in": files2, "out": out2},
                      tool_instance_name="IDFilter-lenient")

Backward compatible—omitting tool_instance_name maintains existing behavior.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Parameter error when using input_TOPP multiple times for the same TOPP tool.</issue_title>
<issue_description>Hi, I'm currently working on a DDA-TMT workflow, where IDFilter is used twice at different stages of the pipeline.
However, I ran into an issue in the parameter configuration UI:
calling input_TOPP("IDFilter") more than once causes a parameter-related error.
From the behavior, it seems that input_TOPP cannot be invoked multiple times
for the same TOPP tool within a single workflow configuration.

Is there a supported pattern for using the same TOPP tool multiple times with different parameters?

</issue_description>

<agent_instructions>Please implement a non-breaking improvement to enable using TOPP tools with different configurations.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Parameter error when using input_TOPP multiple times for the same TOPP tool. #302

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