--- a/COBRAxy/docs/tools/README.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/tools/README.md	Sun Oct 26 19:27:41 2025 +0000
@@ -4,23 +4,16 @@
 
 | Tool | Purpose | Input | Output |
 |------|---------|--------|--------|
-| [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
-| [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values |
-| [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
-| [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
-| [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions |
-| [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
-| [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data |
-| [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
+| [Import Metabolic Model](tools/import-metabolic-model) | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
+| [Export Metabolic Model](tools/export-metabolic-model) | Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
+| [RAS Generator](tools/ras-generator) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
+| [RPS Generator](tools/rps-generator) | Compute reaction propensity scores | Metabolite abundance | RPS values |
+| [MAREA](tools/marea) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
+| [RAS to Bounds](tools/ras-to-bounds) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
+| [Flux Simulation](tools/flux-simulation) | Sample metabolic fluxes | Constrained model | Flux distributions |
+| [Flux to Map](tools/flux-to-map) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
+| [MAREA Cluster](tools/marea-cluster) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
 
-## Common Parameters
-
-All tools share these basic parameters:
-
-- **`-td, --tool_dir`**: COBRAxy installation directory (required)
-- **`-in, --input`**: Input dataset file
-- **`-idop, --output_dir`**: Output directory for results
-- **`-rs, --rules_selector`**: Built-in model (ENGRO2, Recon, HMRcore)
 
 ## Analysis Workflows
 
@@ -74,23 +67,27 @@
 ### Choose Your Analysis Path
 
 **For Pathway Enrichment**
-1. [RAS Generator](ras-generator.md) → Generate activity scores
-2. [RPS Generator](rps-generator.md) → Generate propensity scores (optional)
-3. [MAREA](marea.md) → Statistical analysis and visualization
+1. [RAS Generator](tools/ras-generator) → Generate activity scores
+2. [RPS Generator](tools/rps-generator) → Generate propensity scores (optional)
+3. [MAREA](tools/marea) → Statistical analysis and visualization
 
 **For Flux Analysis**  
-1. [RAS Generator](ras-generator.md) → Generate activity scores
-2. [RAS to Bounds](ras-to-bounds.md) → Apply constraints
-3. [Flux Simulation](flux-simulation.md) → Sample fluxes
-4. [Flux to Map](flux-to-map.md) → Create visualizations
+1. [RAS Generator](tools/ras-generator) → Generate activity scores
+2. [RAS to Bounds](tools/ras-to-bounds) → Apply constraints
+3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
+4. [Flux to Map](tools/flux-to-map) → Create visualizations
 
 **For Model Exploration**
-1. [Model Setting](metabolic-model-setting.md) → Extract model info
+1. [Import Metabolic Model](tools/import-metabolic-model) → Extract model info
 2. Analyze model structure and gene coverage
 
+**For Model Creation**
+1. Create/edit tabular model data
+2. [Export Metabolic Model](tools/export-metabolic-model) → Create SBML/JSON/MAT/YAML model
+
 **For Sample Classification**
 1. Generate RAS/RPS scores
-2. [MAREA Cluster](marea-cluster.md) → Cluster samples
+2. [MAREA Cluster](tools/marea-cluster) → Cluster samples
 
 
 
@@ -98,16 +95,6 @@
 
 ### Common Issues Across Tools
 
-**File Path Problems**
-- Use absolute paths when possible
-- Ensure all input files exist before starting
-- Check write permissions for output directories
-
-**File Issues**
-- Check file paths and permissions
-- Verify input file formats
-- Ensure sufficient disk space
-
 **Model Issues**
 - Verify model file format and gene ID consistency
 - Check gene ID mapping between data and model
@@ -119,7 +106,7 @@
 1. Check individual tool documentation
 2. Review parameter requirements and formats
 3. Test with smaller datasets first
-4. Consult [troubleshooting guide](../troubleshooting.md)
+4. Consult [troubleshooting guide](/troubleshooting.md)
 
 ## Contributing