Workflow Type:  Galaxy
        
  
        
          
            
              
    
      
        
        
    
    
      
        
        
    
    
      
        
        
    
            
          
        
        
      
  
    
      
        
      
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The workflow runs the RetroSynthesis algorithm to generate a collection of heterologous pathways in a host organism of choice, converts them to SBML files, performs analysis on the pathways to then rank the theoretical best performing ones.
Inputs
| ID | Name | Description | Type | 
|---|---|---|---|
| GEM SBML | GEM SBML | n/a | 
 | 
| Maximal Pathway Length | Maximal Pathway Length | n/a | 
 | 
| Target InChI | Target InChI | n/a | 
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| Top Ranking Pathways | Top Ranking Pathways | n/a | 
 | 
Steps
| ID | Name | Description | 
|---|---|---|
| 1 | RetroRules | retrorules | 
| 5 | Make Source | makeSource | 
| 6 | Sink from SBML | rpExtractSink | 
| 7 | RetroPath2.0 | retropath2 | 
| 8 | RP2paths | rp2paths | 
| 9 | Pathways to SBML | rpReader | 
| 10 | Complete Reactions | rpCofactors | 
| 11 | Thermodynamics | rpThermo | 
| 12 | FBA | rpFBA | 
| 13 | Rank Pathways | rpGlobalScore | 
| 14 | Pathway Visualiser | rpVisualiser | 
| 15 | Report | rpReport | 
Outputs
| ID | Name | Description | Type | 
|---|---|---|---|
| _anonymous_output_2 | _anonymous_output_2 | n/a | 
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| _anonymous_output_6 | _anonymous_output_6 | n/a | 
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| _anonymous_output_7 | _anonymous_output_7 | n/a | 
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| _anonymous_output_8 | _anonymous_output_8 | n/a | 
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| _anonymous_output_9 | _anonymous_output_9 | n/a | 
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| _anonymous_output_10 | _anonymous_output_10 | n/a | 
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| _anonymous_output_11 | _anonymous_output_11 | n/a | 
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| _anonymous_output_12 | _anonymous_output_12 | n/a | 
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| _anonymous_output_13 | _anonymous_output_13 | n/a | 
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| _anonymous_output_14 | _anonymous_output_14 | n/a | 
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| _anonymous_output_15 | _anonymous_output_15 | n/a | 
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| _anonymous_output_16 | _anonymous_output_16 | n/a | 
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| _anonymous_output_17 | _anonymous_output_17 | n/a | 
 | 
Version History
Version 1 (earliest) Created 29th May 2020 at 12:19 by Melchior du Lac
Added/updated 1 files
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Created: 29th May 2020 at 12:19
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 https://orcid.org/0000-0002-9984-4689
 https://orcid.org/0000-0002-9984-4689
