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1 # Tool| Tool | Purpose | Input | Output |
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2 |------|---------|--------|---------|
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3 | [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
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4 | [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values |
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5 | [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
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6 | [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
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7 | [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions |
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8 | [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
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9 | [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data |
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10 | [Tabular to Model](tabular-to-model.md) | Create COBRA models | Tabular reaction data | SBML/JSON/MAT/YAML models |
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11 | [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |ation
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12
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13 Complete reference for all COBRAxy tools with parameters, examples, and usage guidelines.
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14
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15 ## Available Tools
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16
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17 | Tool | Purpose | Input | Output |
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18 |------|---------|--------|--------|
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19 | [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
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20 | [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values |
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21 | [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
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22 | [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
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23 | [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions |
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24 | [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
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25 | [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data |
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26 | [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
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27
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28 ## Common Parameters
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29
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30 All tools share these basic parameters:
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31
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32 - **`-td, --tool_dir`**: COBRAxy installation directory (required)
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33 - **`-in, --input`**: Input dataset file
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34 - **`-idop, --output_dir`**: Output directory for results
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35 - **`-rs, --rules_selector`**: Built-in model (ENGRO2, Recon, HMRcore)
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36
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37 ## Analysis Workflows
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38
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39 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps
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40
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41 **Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map
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42
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43 ## Usage Patterns
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44
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45 ### Command Line Usage
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46 ```bash
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47 # Basic pattern for all tools
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48 tool_name -td $(pwd) [tool-specific options]
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49
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50 # Example: Generate RAS scores
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51 ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
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52 ```
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53
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54 ### Python API Usage
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55 ```python
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56 import tool_module
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57
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58 # All tools accept argument lists
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59 args = ['-td', '/path/to/cobraxy', '-in', 'input.tsv', '-out', 'output.tsv']
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60 tool_module.main(args)
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61 ```
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62
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63 ### Galaxy Integration
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64 All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.
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65
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66 ## Parameter Reference
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67
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68 ### File Format Requirements
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69
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70 **Gene Expression Files**
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71 - Format: TSV (tab-separated values)
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72 - Structure: Genes (rows) × Samples (columns)
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73 - First column: Gene IDs (HGNC, Ensembl, etc.)
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74 - Subsequent columns: Expression values
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75
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76 **Metabolite Files**
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77 - Format: TSV (tab-separated values)
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78 - Structure: Metabolites (rows) × Samples (columns)
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79 - First column: Metabolite names
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80 - Subsequent columns: Abundance values
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81
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82 **Model Files**
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83 - Format: SBML (.xml) or tabular rules (.tsv)
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84 - Content: Metabolic network with GPR rules
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85
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86 ### Built-in Models
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87
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88 | Model | Organism | Reactions | Genes | Best For |
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89 |-------|----------|-----------|-------|----------|
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90 | **ENGRO2** | Human | ~2,000 | ~500 | Focused analysis, faster computation |
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91 | **Recon** | Human | ~10,000 | ~2,000 | Comprehensive metabolism |
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92 | **HMRcore** | Human | ~5,000 | ~1,000 | Balanced coverage |
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93
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94 ## Tool Selection Guide
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95
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96 ### Choose Your Analysis Path
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97
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98 **For Pathway Enrichment**
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99 1. [RAS Generator](ras-generator.md) → Generate activity scores
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100 2. [RPS Generator](rps-generator.md) → Generate propensity scores (optional)
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101 3. [MAREA](marea.md) → Statistical analysis and visualization
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102
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103 **For Flux Analysis**
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104 1. [RAS Generator](ras-generator.md) → Generate activity scores
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105 2. [RAS to Bounds](ras-to-bounds.md) → Apply constraints
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106 3. [Flux Simulation](flux-simulation.md) → Sample fluxes
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107 4. [Flux to Map](flux-to-map.md) → Create visualizations
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108
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109 **For Model Exploration**
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110 1. [Model Setting](metabolic-model-setting.md) → Extract model info
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111 2. Analyze model structure and gene coverage
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112
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113 **For Sample Classification**
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114 1. Generate RAS/RPS scores
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115 2. [MAREA Cluster](marea-cluster.md) → Cluster samples
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116
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117
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118
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119 ## Troubleshooting
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120
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121 ### Common Issues Across Tools
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122
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123 **File Path Problems**
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124 - Use absolute paths when possible
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125 - Ensure all input files exist before starting
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126 - Check write permissions for output directories
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127
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128 **File Issues**
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129 - Check file paths and permissions
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130 - Verify input file formats
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131 - Ensure sufficient disk space
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132
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133 **Model Issues**
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134 - Verify model file format and gene ID consistency
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135 - Check gene ID mapping between data and model
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136 - Use built-in models to avoid compatibility issues
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137
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138 ### Getting Help
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139
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140 For tool-specific issues:
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141 1. Check individual tool documentation
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142 2. Review parameter requirements and formats
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143 3. Test with smaller datasets first
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144 4. Consult [troubleshooting guide](../troubleshooting.md)
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145
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146 ## Contributing
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147
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148 Help improve tool documentation:
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149 - Report unclear instructions
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150 - Suggest additional examples
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151 - Contribute usage patterns
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152 - Fix documentation errors
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153
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154 Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips. Select a tool from the sidebar to get started! |
