Create draft metabolic model from pathway and transporter predictions
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reactions
:file
Reactions table from gapseq find
*-all-Reactions.tbl
transporters
:file
Transporters CSV file from gapseq find-transport
*-Transporter.tbl
pathways
:file
Pathways CSV file from gapseq find
*-all-Pathways.tbl
Output
name:type
description
pattern
draft
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.RDS
:file
Draft metabolic model in RDS format
*.RDS
xml
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.xml
:file
Draft metabolic model in SBML XML format
*.xml
log
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log
:file
Log files from gapseq draft
*.log
versions_gapseq
${task.process}
:string
The name of the process
gapseq
:string
The name of the tool
gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
gapseq
:string
The name of the tool
gapseq -v 2>&1 | grep -oP "\d+\.\d+\.\d+"
:eval
The expression to obtain the version of the tool
Tools
gapseq
AGPL-3.0-only
gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation.
The draft command constructs a draft metabolic model from pathway and transporter predictions.
