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1 # RPS Generator
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2
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3 Compute Reaction Presence Scores (RPS) from metabolite abundance data.
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4
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5 ## Overview
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6
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7 RPS Generator calculates reaction presence scores based on metabolite availability in reaction formulas.
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8
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9 ## Galaxy Interface
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10
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11 In Galaxy: **COBRAxy → RPS Generator**
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12
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13 1. Select built-in model or upload custom reactions
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14 2. Upload metabolite abundance data
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15 3. Click **Execute**
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16
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17 ## Usage
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18
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19 ```bash
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20 rps_generator -rs ENGRO2 \
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21 -in metabolite_data.tsv \
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22 -rps rps_scores.tsv \
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23 -ol rps_generation.log
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24 ```
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25
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26 ## Parameters
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27
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28 | Parameter | Flag | Description | Default |
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29 |-----------|------|-------------|---------|
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30 | Rules Selector | `-rs` | ENGRO2, Recon, or Custom | ENGRO2 |
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31 | Input Data | `-in` | Metabolite abundance TSV file | - |
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32 | Output RPS | `-rps` | Output RPS scores file | - |
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33 | Output Log | `-ol` | Log file | - |
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34 | Custom Rules | `-rl` | Custom reaction formulas file | - |
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35
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36 ## Input Format
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37
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38 Metabolite data file (TSV):
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39
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40 ```
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41 Metabolite Sample1 Sample2 Sample3
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42 glc_c 2.5 1.8 3.2
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43 atp_c 5.2 4.9 5.8
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44 pyr_c 1.5 2.1 1.8
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45 ```
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46
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47 **File Format Notes:**
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48 - Use **tab-separated** values (TSV)
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49 - First row must contain column headers (Metabolite, Sample names)
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50 - Metabolite names must include compartment suffix (e.g., _c, _m, _e)
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51 - Numeric values only for abundance data
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52
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53 ## Output Format
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54
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55 ```
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56 Reaction Sample1 Sample2 Sample3
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57 R00001 1.25 0.95 1.42
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58 R00002 0.85 1.15 0.92
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59 ```
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60
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61 ## Examples
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62
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63 ### Basic Usage
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64
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65 ```bash
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66 rps_generator -rs ENGRO2 \
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67 -in metabolites.tsv \
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68 -rps rps_scores.tsv
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69 ```
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70
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71 ### Custom Reactions
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72
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73 ```bash
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74 rps_generator -rs Custom \
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75 -rl custom_reactions.csv \
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76 -in metabolites.tsv \
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77 -rps rps_scores.tsv
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78 ```
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79
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80 ## Troubleshooting
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81
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82 | Error | Solution |
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83 |-------|----------|
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84 | "Metabolite not found" | Check metabolite nomenclature |
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85 | "Invalid formula" | Verify reaction formula syntax |
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86
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87 ## See Also
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88
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89 - [MAREA](tools/marea)
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90 - [RAS Generator](tools/ras-generator)
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91 - [Built-in Models](reference/built-in-models)
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