Add boolean flag parameter support in CommandExecutor.run_topp()

Handle POSIX-style boolean flags in TOPP tool parameters where 'true'
emits -flag only (no value) and 'false' skips the parameter entirely.
This fixes tools like FLASHDeconv and FLASHTnT that expect flag-style
boolean parameters rather than -flag true/-flag false.

https://claude.ai/code/session_01R4Uj1R6TMZ6biZ6Ks9HT4C

Author: claude

src/workflow/CommandExecutor.py

@@ -284,14 +284,21 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
             # Add non-default TOPP tool parameters
             if tool in params.keys():
                 for k, v in params[tool].items():
-                    command += [f"-{k}"]
-                    # Skip only empty strings (pass flag with no value)
-                    # Note: 0 and 0.0 are valid values, so use explicit check
-                    if v != "" and v is not None:
-                        if isinstance(v, str) and "\n" in v:
-                            command += v.split("\n")
-                        else:
-                            command += [str(v)]
+                    # Handle boolean flag parameters:
+                    # 'true' → emit -flag only, 'false' → skip entirely
+                    if isinstance(v, str) and v.lower() == "true":
+                        command += [f"-{k}"]
+                    elif isinstance(v, str) and v.lower() == "false":
+                        continue
+                    else:
+                        command += [f"-{k}"]
+                        # Skip only empty strings (pass flag with no value)
+                        # Note: 0 and 0.0 are valid values, so use explicit check
+                        if v != "" and v is not None:
+                            if isinstance(v, str) and "\n" in v:
+                                command += v.split("\n")
+                            else:
+                                command += [str(v)]
             # Add custom parameters
             for k, v in custom_params.items():
                 command += [f"-{k}"]