docs: add parameter presets documentation

Document the new presets feature in three locations:

- docs/user_guide.md: User-facing guide on how to use preset buttons
- docs/build_app.md: Developer guide on presets.json format and structure
- docs/toppframework.py: Interactive TOPP framework docs with st.help()

https://claude.ai/code/session_01BnipAqTf16J7kJVfnzah2U

Author: claude

docs/build_app.md

@@ -22,6 +22,73 @@ value=params["example-y-dimension"], step=1, key="example-y-dimension")
 save_params()
 ```
 
+- **Parameter Presets**
+: Presets provide quick configuration options for workflows. Define presets in `presets.json` at the repository root. Presets are automatically displayed as buttons in the parameter section when defined for a workflow.
+
+## Parameter Presets
+
+Presets allow users to quickly apply optimized parameter configurations. They are defined in `presets.json` at the repository root.
+
+### presets.json Format
+
+```json
+{
+  "workflow-name": {
+    "Preset Name": {
+      "_description": "Tooltip description shown on hover",
+      "TOPPToolName": {
+        "algorithm:section:param_name": value
+      },
+      "_general": {
+        "custom_param_key": value
+      }
+    }
+  }
+}
+```
+
+### Structure Details
+
+| Key | Description |
+|-----|-------------|
+| `workflow-name` | Must match the workflow name (lowercase, hyphens instead of spaces). E.g., "TOPP Workflow" → "topp-workflow" |
+| `Preset Name` | Display name for the preset button |
+| `_description` | Optional tooltip text (keys prefixed with `_` are metadata) |
+| `TOPPToolName` | Dictionary of TOPP tool parameters to override |
+| `_general` | Dictionary of general workflow parameters (custom `input_widget` keys) |
+
+### Example
+
+```json
+{
+  "topp-workflow": {
+    "High Sensitivity": {
+      "_description": "Optimized for detecting low-abundance features",
+      "FeatureFinderMetabo": {
+        "algorithm:common:noise_threshold_int": 500.0,
+        "algorithm:common:chrom_peak_snr": 2.0
+      }
+    },
+    "Fast Analysis": {
+      "_description": "Quick processing with relaxed parameters",
+      "FeatureFinderMetabo": {
+        "algorithm:common:noise_threshold_int": 2000.0
+      },
+      "FeatureLinkerUnlabeledKD": {
+        "algorithm:link:rt_tol": 60.0
+      }
+    }
+  }
+}
+```
+
+### How It Works
+
+1. Preset buttons automatically appear in `parameter_section()` via `StreamlitUI.preset_buttons()`
+2. Only presets matching the current workflow name are displayed
+3. Clicking a preset updates `params.json` and refreshes the UI
+4. If no `presets.json` exists or no presets match the workflow, no buttons are shown
+
 ## Code structure
 - The main file `app.py` defines page layout.
 - **Pages** must be placed in the `content` directory.

docs/toppframework.py

@@ -3,6 +3,7 @@
 from src.workflow.StreamlitUI import StreamlitUI
 from src.workflow.FileManager import FileManager
 from src.workflow.CommandExecutor import CommandExecutor
+from src.workflow.ParameterManager import ParameterManager
 from inspect import getsource
 
 def content():
@@ -136,6 +137,52 @@ def content():
         st.help(StreamlitUI.select_input_file)
         st.help(StreamlitUI.input_TOPP)
         st.help(StreamlitUI.input_python)
+
+    st.markdown(
+        """
+## Parameter Presets
+
+Presets provide a way to offer users quick parameter configuration options for common analysis scenarios.
+
+### Enabling Presets
+
+1. Create a `presets.json` file at the repository root
+2. Add preset definitions for your workflow (workflow name must be normalized: lowercase with hyphens)
+3. Presets automatically appear in the parameter section via `self.ui.preset_buttons()`
+
+### presets.json Structure
+
+```json
+{
+  "your-workflow-name": {
+    "Preset Display Name": {
+      "_description": "Tooltip text for the button",
+      "TOPPToolName": {
+        "algorithm:param:path": value
+      },
+      "_general": {
+        "custom_widget_key": value
+      }
+    }
+  }
+}
+```
+
+### Key Points
+
+- **Workflow matching**: Workflow name is normalized (lowercase, hyphens for spaces). "TOPP Workflow" → "topp-workflow"
+- **TOPP parameters**: Use the full parameter path (e.g., `algorithm:common:noise_threshold_int`)
+- **General parameters**: Use `_general` for custom `input_widget` parameters
+- **Descriptions**: Keys prefixed with `_` are metadata (not applied as parameters)
+- **Opt-in feature**: No `presets.json` = no buttons shown (backward compatible)
+"""
+    )
+
+    with st.expander("**Code documentation**", expanded=True):
+        st.help(StreamlitUI.preset_buttons)
+        st.help(ParameterManager.load_presets)
+        st.help(ParameterManager.apply_preset)
+
     st.markdown(
         """
 ## Building the Workflow

docs/user_guide.md

@@ -55,4 +55,23 @@ To get started:
 4. Run the analysis.
 5. View and download your results.
 
-For more detailed information on each step, refer to the specific sections of this guide.
+For more detailed information on each step, refer to the specific sections of this guide.
+
+## Parameter Presets
+
+Parameter presets allow you to quickly apply optimized parameter configurations for common analysis scenarios. When available, preset buttons appear on the parameter configuration page.
+
+### Using Presets
+
+1. Navigate to the parameter configuration page
+2. Look for the **Parameter Presets** section below the "Show advanced parameters" toggle
+3. Hover over a preset button to see its description
+4. Click a preset to apply its optimized parameters
+5. A confirmation message will appear when the preset is applied
+
+### What Presets Do
+
+- Presets override specific tool parameters with pre-configured values
+- Only the parameters defined in the preset are changed; other parameters remain at their current values
+- You can still modify individual parameters after applying a preset
+- Use **Load default parameters** to reset all parameters to their original defaults