Workflow Entry: Download pathways for external references list (Taverna 2)

Created at: 03/02/09 @ 12:46:13 Last updated: 03/02/09 @ 12:46:14

Version 1 (of 1)

Version created on: 03/02/09 @ 12:46:13 by: Thomaskelder | Revision comments Expand

Title: Download pathways for external references list (Taverna 2)

Type: Taverna 2

Preview

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Description

Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Download

Download Workflow File/Package (T2FLOW)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/642/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (3)

Name	Description
xreflist
output_path
file_type

Processors (11)

Name	Type	Description
createPath	beanshell
createFileName	beanshell
count	beanshell
splitLines	localworker
readXrefList	localworker
clone_list	workflow
find_pathways_by_xref	workflow
write_pathway	workflow
splitLines_regex_defaultValue	stringconstant
find_pathways_by_xref_system_code_defaultValue	stringconstant
write_pathway_revision_defaultValue	stringconstant

Beanshells (5)

Name	Inputs	Outputs
createPath	output_path xref	path_name
createFileName	pathway_name path_name pathway_species	file_name
count	list	count
Clone	copy_number input	clones
writeFile	data fileName

Outputs (1)

Name	Description
written_files

Datalinks (18)

Sink	Source
createPath:output_path	output_path
createPath:xref	splitLines:split
createFileName:pathway_name	find_pathways_by_xref:pathway_names
createFileName:pathway_species	find_pathways_by_xref:pathway_species
createFileName:path_name	clone_list:clones
count:list	find_pathways_by_xref:pathway_names
splitLines:string	readXrefList:filecontents
splitLines:regex	splitLines_regex_defaultValue:value
readXrefList:fileurl	xreflist
clone_list:copy_number	count:count
clone_list:input	createPath:path_name
find_pathways_by_xref:system_code	find_pathways_by_xref_system_code_defaultValue:value
find_pathways_by_xref:identifier	splitLines:split
write_pathway:file_type	file_type
write_pathway:file_name	createFileName:file_name
write_pathway:pathway_id	find_pathways_by_xref:pathway_ids
write_pathway:revision	write_pathway_revision_defaultValue:value
written_files	write_pathway:writtenFile