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492
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1 Complete reference for all COBRAxy tools with parameters, examples, and usage guidelines.
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2
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3 ## Available Tools
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4
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5 | Tool | Purpose | Input | Output |
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6 |------|---------|--------|--------|
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7 | [RAS Generator](ras-generator.md) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
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8 | [RPS Generator](rps-generator.md) | Compute reaction propensity scores | Metabolite abundance | RPS values |
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9 | [MAREA](marea.md) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
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10 | [RAS to Bounds](ras-to-bounds.md) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
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11 | [Flux Simulation](flux-simulation.md) | Sample metabolic fluxes | Constrained model | Flux distributions |
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12 | [Flux to Map](flux-to-map.md) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
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13 | [Model Setting](metabolic-model-setting.md) | Extract model components | SBML/JSON/MAT/YML model | Tabular model data |
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14 | [MAREA Cluster](marea-cluster.md) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
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15
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16 ## Common Parameters
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17
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18 All tools share these basic parameters:
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19
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20 - **`-td, --tool_dir`**: COBRAxy installation directory (required)
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21 - **`-in, --input`**: Input dataset file
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22 - **`-idop, --output_dir`**: Output directory for results
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23 - **`-rs, --rules_selector`**: Built-in model (ENGRO2, Recon, HMRcore)
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24
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25 ## Analysis Workflows
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26
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27 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps
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28
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29 **Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map
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30
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31 ## Usage Patterns
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32
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538
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33 ### Galaxy Integration
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34 All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.
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35
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492
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36 ### Command Line Usage
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37 ```bash
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38 # Basic pattern for all tools
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39 tool_name -td $(pwd) [tool-specific options]
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40
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41 # Example: Generate RAS scores
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42 ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
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43 ```
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44
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45 ## Parameter Reference
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46
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47 ### File Format Requirements
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48
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49 **Gene Expression Files**
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50 - Format: TSV (tab-separated values)
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51 - Structure: Genes (rows) × Samples (columns)
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52 - First column: Gene IDs (HGNC, Ensembl, etc.)
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53 - Subsequent columns: Expression values
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54
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55 **Metabolite Files**
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56 - Format: TSV (tab-separated values)
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57 - Structure: Metabolites (rows) × Samples (columns)
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58 - First column: Metabolite names
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59 - Subsequent columns: Abundance values
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60
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61 **Model Files**
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62 - Format: SBML (.xml) or tabular rules (.tsv)
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63 - Content: Metabolic network with GPR rules
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64
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65 ### Built-in Models
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66
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67 | Model | Organism | Reactions | Genes | Best For |
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68 |-------|----------|-----------|-------|----------|
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69 | **ENGRO2** | Human | ~500 | ~500 | Focused analysis, faster computation |
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70 | **RECON3D** | Human | ~10,000 | ~2,000 | Comprehensive metabolism |
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492
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71
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72 ## Tool Selection Guide
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73
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74 ### Choose Your Analysis Path
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75
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76 **For Pathway Enrichment**
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77 1. [RAS Generator](ras-generator.md) → Generate activity scores
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78 2. [RPS Generator](rps-generator.md) → Generate propensity scores (optional)
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79 3. [MAREA](marea.md) → Statistical analysis and visualization
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80
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81 **For Flux Analysis**
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82 1. [RAS Generator](ras-generator.md) → Generate activity scores
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83 2. [RAS to Bounds](ras-to-bounds.md) → Apply constraints
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84 3. [Flux Simulation](flux-simulation.md) → Sample fluxes
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85 4. [Flux to Map](flux-to-map.md) → Create visualizations
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86
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87 **For Model Exploration**
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88 1. [Model Setting](metabolic-model-setting.md) → Extract model info
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89 2. Analyze model structure and gene coverage
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90
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91 **For Sample Classification**
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92 1. Generate RAS/RPS scores
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93 2. [MAREA Cluster](marea-cluster.md) → Cluster samples
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94
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95
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96
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97 ## Troubleshooting
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98
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99 ### Common Issues Across Tools
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100
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101 **File Path Problems**
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102 - Use absolute paths when possible
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103 - Ensure all input files exist before starting
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104 - Check write permissions for output directories
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105
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106 **File Issues**
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107 - Check file paths and permissions
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108 - Verify input file formats
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109 - Ensure sufficient disk space
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110
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111 **Model Issues**
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112 - Verify model file format and gene ID consistency
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113 - Check gene ID mapping between data and model
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114 - Use built-in models to avoid compatibility issues
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115
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116 ### Getting Help
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117
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118 For tool-specific issues:
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119 1. Check individual tool documentation
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120 2. Review parameter requirements and formats
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121 3. Test with smaller datasets first
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122 4. Consult [troubleshooting guide](../troubleshooting.md)
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123
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124 ## Contributing
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125
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126 Help improve tool documentation:
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127 - Report unclear instructions
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128 - Suggest additional examples
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129 - Contribute usage patterns
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130 - Fix documentation errors
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131
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132 Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips. Select a tool from the sidebar to get started! |
