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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 | Galaxy Tool | Python script | Purpose | Input | Output |
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6 |------|---------|---------|--------|--------|
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7 | [Import Metabolic Model](tools/import-metabolic-model) | importMetabolicModel | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
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8 | [Export Metabolic Model](tools/export-metabolic-model) | exportMetabolicModel |Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
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9 | [Expression2RAS](tools/ras-generator) | ras_generator | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
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10 | [Expression2RPS](tools/rps-generator) | rps_generator | Compute reaction propensity scores | Metabolite abundance | RPS values |
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11 | [Metabolic Reaction Enrichment Analysis](tools/marea) | marea | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
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12 | [RAS2Bounds](tools/ras-to-bounds) | ras_to_bounds | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
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13 | [Flux Simulation](tools/flux-simulation) | flux_simulation | Sample metabolic fluxes | Constrained model | Flux distributions |
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14 | [Metabolic Flux Enrichment Analysis](tools/flux-to-map) | flux_to_map | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
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15 | [Cluster Analysis](tools/marea-cluster) | marea_cluster | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
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16
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17 ## Analysis Workflows
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18
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19 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps
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20
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21 **Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map
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22
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23 ## Usage Patterns
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24
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538
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25 ### Galaxy Integration
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26 All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.
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27
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492
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28 ### Command Line Usage
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29 ```bash
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30 # Basic pattern for all tools
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31 tool_name [tool-specific options]
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32
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33 # Example: Generate RAS scores
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34 ras_generator -in expression.tsv -ra ras_output.tsv -rs ENGRO2
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35 ```
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36
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37 ## Tool Selection Guide
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38
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39 ### Choose Your Analysis Path
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40
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41 **For Pathway Enrichment**
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42 1. [RAS Generator](tools/ras-generator) → Generate activity scores
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43 2. [RPS Generator](tools/rps-generator) → Generate propensity scores (optional)
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44 3. [MAREA](tools/marea) → Statistical analysis and visualization
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45
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46 **For Flux Analysis**
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542
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47 1. [RAS Generator](tools/ras-generator) → Generate activity scores
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48 2. [RAS to Bounds](tools/ras-to-bounds) → Apply constraints
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49 3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
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50 4. [Flux to Map](tools/flux-to-map) → Create visualizations
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51
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542
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52 **For Model Creation**
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53 1. Create/edit tabular model data
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54 2. [Export Metabolic Model](tools/export-metabolic-model) → Create SBML/JSON/MAT/YAML model
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55
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492
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56 ## Troubleshooting
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57
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58 ### Common Issues Across Tools
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59
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60 **Model Issues**
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61 - Verify model file format and gene ID consistency
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62 - Check gene ID mapping between data and model
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63
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64 ### Getting Help
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65
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66 For tool-specific issues:
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67 1. Check individual tool documentation
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68 2. Review parameter requirements and formats
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69 3. Test with smaller datasets first
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70 4. Consult [troubleshooting guide](troubleshooting)
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71
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72 ## Contributing
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73
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74 Help improve tool documentation:
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75 - Report unclear instructions
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76 - Suggest additional examples
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77 - Contribute usage patterns
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78 - Fix documentation errors
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79
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80 Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips.
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