The introduction of tool_instance_name to support multiple instances of the same TOPP tool (e.g., duplicate IDFilter calls) has caused a side effect when executing the save_parameters method.

Specifically, during the execution of the save_parameters loop, the tool_instance_name is being passed into the create_ini method. This results in an invalid tool name causing create_ini to fail.

for tool in current_topp_tools:
            if not self.create_ini(tool):
                # Could not create ini file - skip this tool
                continue