support flag parameters without valuesAllow flags to work with only key names, omitting values.

.gitignore

@@ -13,3 +13,4 @@ gdpr_consent/node_modules/
 *~
 .streamlit/secrets.toml
 docs/superpowers/
+.venv/

src/workflow/CommandExecutor.py

@@ -5,7 +5,7 @@
 import threading
 from pathlib import Path
 from .Logger import Logger
-from .ParameterManager import ParameterManager
+from .ParameterManager import ParameterManager, bool_param_paths_from_param_xml_ini
 import sys
 import importlib.util
 import json
@@ -216,7 +216,7 @@ def read_stderr():
         stdout_thread.join()
         stderr_thread.join()
 
-    def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> bool:
+    def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}, tool_instance_name: str = None) -> bool:
         """
         Constructs and executes commands for the specified tool OpenMS TOPP tool based on the given
         input and output configurations. Ensures that all input/output file lists
@@ -234,6 +234,10 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
             tool (str): The executable name or path of the tool.
             input_output (dict): A dictionary specifying the input/output parameter names (as key) and their corresponding file paths (as value).
             custom_params (dict): A dictionary of custom parameters to pass to the tool.
+            tool_instance_name (str, optional): Key for ``params.json`` when it differs
+                from ``tool`` (e.g. multiple instances). Defaults to ``tool``.
+            Custom parameters whose keys appear in the tool's ParamXML ``type="bool"``
+            entries are passed as valueless CLI flags (``-name`` only when enabled).
 
         Returns:
             bool: True if all commands succeeded, False if any failed.
@@ -261,8 +265,15 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
 
         commands = []
 
-        # Load parameters for non-defaults
         params = self.parameter_manager.get_parameters_from_json()
+
+        topp_tool_ini_path = Path(self.parameter_manager.ini_dir, f"{tool}.ini")
+        # Keys of type="bool" in the .ini: TOPP treats these as on/off flags (omit value when off)
+        topp_bool_flag_param_keys = (
+            bool_param_paths_from_param_xml_ini(topp_tool_ini_path, tool)
+            if topp_tool_ini_path.exists()
+            else set()
+        )
         # Construct commands for each process
         for i in range(n_processes):
             command = [tool]
@@ -284,6 +295,16 @@ 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():
+
+                    if k in topp_bool_flag_param_keys and v != "":
+                    # CLI flag: include "-k" only when enabled
+                        if isinstance(v, str):
+                            is_enabled = v.lower() == "true"
+                        else:
+                            is_enabled = bool(v)
+                        if is_enabled:
+                            command += [f"-{k}"]
+                        continue
                     command += [f"-{k}"]
                     # Skip only empty strings (pass flag with no value)
                     # Note: 0 and 0.0 are valid values, so use explicit check
@@ -295,6 +316,7 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
             # Add custom parameters
             for k, v in custom_params.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:

src/workflow/ParameterManager.py

@@ -3,8 +3,52 @@
 import shutil
 import subprocess
 import streamlit as st
+import xml.etree.ElementTree as ET
 from pathlib import Path
 
+
+def bool_param_paths_from_param_xml_ini(ini_path: Path, tool_stem: str) -> set[str]:
+    """
+    Return short parameter paths for every ``<ITEM type="bool">`` in a ParamXML .ini file.
+
+    Paths match the suffix after ``Tool:1:`` in pyOpenMS (e.g. ``algorithm:epd:masstrace_snr_filtering``).
+    """
+    try:
+        root = ET.parse(ini_path).getroot()
+    except (ET.ParseError, OSError):
+        return set()
+
+    def local_tag(el: ET.Element) -> str:
+        t = el.tag
+        return t.rsplit("}", 1)[-1] if isinstance(t, str) and "}" in t else str(t)
+
+    out: set[str] = set()
+
+    def walk(el: ET.Element, parts: tuple[str, ...]) -> None:
+        for ch in el:
+            lt = local_tag(ch)
+            if lt == "NODE":
+                nm = ch.get("name") or ""
+                walk(ch, parts + (nm,))
+            elif lt == "ITEM" and (ch.get("type") or "").lower() == "bool":
+                nm = ch.get("name") or ""
+                segs = [p for p in parts if p]
+                if nm:
+                    segs.append(nm)
+                if not segs:
+                    continue
+                # Strip tool root NODE name and instance NODE "1" (not part of pyOpenMS short keys)
+                while segs and segs[0] in (tool_stem, "1"):
+                    segs.pop(0)
+                if segs:
+                    out.add(":".join(segs))
+
+    for ch in root:
+        if local_tag(ch) == "NODE":
+            walk(ch, ())
+    return out
+
+
 class ParameterManager:
     """
     Manages the parameters for a workflow, including saving parameters to a JSON file,
@@ -29,6 +73,29 @@ def __init__(self, workflow_dir: Path, workflow_name: str = None):
         # Store workflow name for preset loading; default to directory stem if not provided
         self.workflow_name = workflow_name or workflow_dir.stem
 
+    def bool_pairs_session_key(self) -> str:
+        """Session state key holding a set of (tool name, param path) for bool TOPP params."""
+        return f"{self.ini_dir.parent.stem}-topp-bool-pairs"
+
+    def get_bool_param_pairs(self) -> set:
+        """Return the cached set of (tool, param path) bool params; empty set if none."""
+        return st.session_state.get(self.bool_pairs_session_key(), set())
+
+    def _merge_bool_params_from_ini(self, tool: str) -> None:
+        """Load tool.ini (XML) and merge type=bool parameter paths into session_state."""
+        ini_path = Path(self.ini_dir, f"{tool}.ini")
+        if not ini_path.exists():
+            return
+        try:
+            sk = self.bool_pairs_session_key()
+            if sk not in st.session_state:
+                st.session_state[sk] = set()
+            for short in bool_param_paths_from_param_xml_ini(ini_path, tool):
+                st.session_state[sk].add((tool, short))
+        except RuntimeError:
+            # No Streamlit session (e.g. plain `python` import)
+            pass
+
     def create_ini(self, tool: str) -> bool:
         """
         Create an ini file for a TOPP tool if it doesn't exist.
@@ -41,11 +108,14 @@ def create_ini(self, tool: str) -> bool:
         """
         ini_path = Path(self.ini_dir, tool + ".ini")
         if ini_path.exists():
+            self._merge_bool_params_from_ini(tool)
             return True
         try:
             subprocess.call([tool, "-write_ini", str(ini_path)])
         except FileNotFoundError:
             return False
+        if ini_path.exists():
+            self._merge_bool_params_from_ini(tool)
         return ini_path.exists()
 
     def save_parameters(self) -> None: