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Introduction Version

Draft recon

Deprecated TASK
Deprecated since the version : 0.5.0
Please reconsider to user the laters version of DraftRecon
Typing name :  TASK.gws_gena.DraftRecon Brick :  gws_gena v

Draft network reconstruction

DraftRecon task.

This task performs a draft reconstruction of a metabolic network using a list of EC numbers or taxonomy IDs.

Input

Table of EC numbers
Table of EC numbers
Optional
Biomass reaction table
Stoichiometry table describing the biomass composition
Optional
Medium table
Table of culture medium composition
Optional

Output

Network
Metabolic network

Configuration

unique_name

Optional

The unique name of the network. Required to uniquely identify taxa in microbial communities

Type : stringDefault value : YuiP

tax_id

Optional

The NCBI taxonomy id. For example: `tax_id = 562` for E. Coli

Type : string

tax_search_method

Optional

If 'bottom_up', the algorithm will to traverse the taxonomy tree to search at higher taxonomy levels until a reaction is found. If `none`, the algorithm will only search at the given taxonomy level given by `tax_id`

Type : stringAllowed values : none  bottom_up  Default value : bottom_up