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Download pathways for external references list (Taverna 2)

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

Created at: 03/02/09 @ 12:46:13

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

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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.

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Option 1:

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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)

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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Thomask...

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Thomaskelder

Information Attributions (0)

(Workflows/Files)

None

Information Tags (5)

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Information Shared with Groups (0)

None

Information Featured In Packs (1)

WikiPathways workflows

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Information Ratings (0)

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0.0 / 5

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Information Attributed By (0)

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None

Information Favourited By (0)

No one

Information Statistics

510 viewings

902 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Download pathways for external references list (Taverna 2)

Created on: Tuesday 03 February 2009 @ 12:46:13 (GMT)

Created by: Thomaskelder

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Other workflows that use similar services (2)

Taverna 1

Original Uploader

Thomask...

Get pathways by external reference (v3)

Created: 13/01/10 @ 12:21:59

Credits: Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 159 times | Downloaded: 59 times

Tags (5):