Pathway Ranker
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

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.

SEEK ID: https://workflowhub.eu/workflows/25?version=1

Inputs

ID	Name	Description	Type
GEM SBML	GEM SBML	n/a	File
Maximal Pathway Length	Maximal Pathway Length	n/a	int
Target InChI	Target InChI	n/a	string
Top Ranking Pathways	Top Ranking Pathways	n/a	int

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	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
_anonymous_output_12	_anonymous_output_12	n/a	File
_anonymous_output_13	_anonymous_output_13	n/a	File
_anonymous_output_14	_anonymous_output_14	n/a	File
_anonymous_output_15	_anonymous_output_15	n/a	File
_anonymous_output_16	_anonymous_output_16	n/a	File
_anonymous_output_17	_anonymous_output_17	n/a	File