comparison COBRAxy/docs/tools/README.md @ 538:fd53d42348bd draft

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# Tool| 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 |
| [Tabular to Model](tabular-to-model.md) | Create COBRA models | Tabular reaction data | SBML/JSON/MAT/YAML models |
| [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |ation

Complete reference for all COBRAxy tools with parameters, examples, and usage guidelines.

## Available Tools

| Tool | Purpose | Input | Output |

**Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map

## Usage Patterns

### Command Line Usage
```bash
# Basic pattern for all tools
tool_name -td $(pwd) [tool-specific options]

# Example: Generate RAS scores
ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
```

### Python API Usage
```python
import tool_module

# All tools accept argument lists
args = ['-td', '/path/to/cobraxy', '-in', 'input.tsv', '-out', 'output.tsv']
tool_module.main(args)
```

### Galaxy Integration
All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.

## Parameter Reference

### File Format Requirements

### Built-in Models

| Model | Organism | Reactions | Genes | Best For |
|-------|----------|-----------|-------|----------|
| **ENGRO2** | Human | ~2,000 | ~500 | Focused analysis, faster computation |
| **Recon** | Human | ~10,000 | ~2,000 | Comprehensive metabolism |
| **HMRcore** | Human | ~5,000 | ~1,000 | Balanced coverage |

## Tool Selection Guide

### Choose Your Analysis Path

538:fd53d42348bd

Complete reference for all COBRAxy tools with parameters, examples, and usage guidelines.

## Available Tools

| Tool | Purpose | Input | Output |

**Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map

## Usage Patterns

### Galaxy Integration
All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.

### Command Line Usage
```bash
# Basic pattern for all tools
tool_name -td $(pwd) [tool-specific options]

# Example: Generate RAS scores
ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
```

## Parameter Reference

### File Format Requirements

### 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