--- a/COBRAxy/docs/tools/README.md	Mon Oct 27 12:33:08 2025 +0000
+++ b/COBRAxy/docs/tools/README.md	Tue Oct 28 10:44:07 2025 +0000
@@ -2,18 +2,17 @@
 
 ## Available Tools
 
-| Tool | Purpose | Input | Output |
-|------|---------|--------|--------|
-| [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 |
-
+| Galaxy Tool | Python script | Purpose | Input | Output |
+|------|---------|---------|--------|--------|
+| [Import Metabolic Model](tools/import-metabolic-model) | importMetabolicModel | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
+| [Export Metabolic Model](tools/export-metabolic-model) | exportMetabolicModel |Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
+| [Expression2RAS](tools/ras-generator) | ras_generator | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
+| [Expression2RPS](tools/rps-generator) | rps_generator | Compute reaction propensity scores | Metabolite abundance | RPS values |
+| [Metabolic Reaction Enrichment Analysis](tools/marea) | marea | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
+| [RAS2Bounds](tools/ras-to-bounds) | ras_to_bounds | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
+| [Flux Simulation](tools/flux-simulation) | flux_simulation | Sample metabolic fluxes | Constrained model | Flux distributions |
+| [Metabolic Flux Enrichment Analysis](tools/flux-to-map) | flux_to_map | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
+| [Cluster Analysis](tools/marea-cluster) | marea_cluster | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
 
 ## Analysis Workflows
 
@@ -29,39 +28,12 @@
 ### Command Line Usage
 ```bash
 # Basic pattern for all tools
-tool_name -td $(pwd) [tool-specific options]
+tool_name [tool-specific options]
 
 # Example: Generate RAS scores
-ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
+ras_generator -in expression.tsv -ra ras_output.tsv -rs ENGRO2
 ```
 
-## Parameter Reference
-
-### File Format Requirements
-
-**Gene Expression Files**
-- Format: TSV (tab-separated values)
-- Structure: Genes (rows) × Samples (columns)
-- First column: Gene IDs (HGNC, Ensembl, etc.)
-- Subsequent columns: Expression values
-
-**Metabolite Files**
-- Format: TSV (tab-separated values)  
-- Structure: Metabolites (rows) × Samples (columns)
-- First column: Metabolite names
-- Subsequent columns: Abundance values
-
-**Model Files**
-- Format: SBML (.xml) or tabular rules (.tsv)
-- Content: Metabolic network with GPR rules
-
-### Built-in Models
-
-| Model | Organism | Reactions | Genes | Best For |
-|-------|----------|-----------|-------|----------|
-| **ENGRO2** | Human | ~500 | ~500 | Focused analysis, faster computation |
-| **RECON3D** | Human | ~10,000 | ~2,000 | Comprehensive metabolism |
-
 ## Tool Selection Guide
 
 ### Choose Your Analysis Path
@@ -77,20 +49,10 @@
 3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
 4. [Flux to Map](tools/flux-to-map) → Create visualizations
 
-**For Model Exploration**
-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](tools/marea-cluster) → Cluster samples
-
-
-
 ## Troubleshooting
 
 ### Common Issues Across Tools
@@ -98,7 +60,6 @@
 **Model Issues**
 - Verify model file format and gene ID consistency
 - Check gene ID mapping between data and model
-- Use built-in models to avoid compatibility issues
 
 ### Getting Help
 
@@ -106,7 +67,7 @@
 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)
 
 ## Contributing
 
@@ -116,4 +77,4 @@
 - Contribute usage patterns
 - Fix documentation errors
 
-Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips. Select a tool from the sidebar to get started!
\ No newline at end of file
+Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips.