Write pathway to disk

Created: 2008-11-14 14:21:12 Last updated: 2008-11-14 14:21:13

Download Workflow

Downloads and writes a pathway from WikiPathways to a local disk in the given file type.

Preview

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/392/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (5)

Name	Description
pathway_name	The name of the pathway (e.g. "Apoptosis").
pathway_species	The species of the pathway (e.g. "Homo sapiens"). See http://www.wikipathways.org for a list of available species.
file_type	The type of the file to write. This can be one of: - gpml (xml format, for use in WikiPathways, PathVisio, Cytoscape) - png (rasterized image format) - svg (vector image format) - pdf (portable document format) - pwf (for use in Eu.Gene) - txt (a text file containing a list of external references for the genes/proteins/metabolites on the pathway)
revision	The version of the pathway to download. Use '0' for the latest revision.
file_name	The name of the file to write the pathway to, without the file extension (this will be derived form the file type).

Processors (6)

Name	Type	Description
concat_filetype	local
concat_dot	local
writeFile	beanshell
getPathwayAsOutput	local
getPathwayAsInput	local
getPathwayAs	arbitrarywsdl

Beanshells (1)

Name	Description	Inputs	Outputs
writeFile		data fileName

Outputs (1)

Name	Description
writtenFile	The file that was written.

Links (12)

Source	Sink
file_name	concat_dot:string1
file_type	getPathwayAsInput:fileType
concat_dot:output	concat_filetype:string1
file_type	concat_filetype:string2
getPathwayAs:parameters	getPathwayAsOutput:input
getPathwayAsInput:output	getPathwayAs:parameters
pathway_name	getPathwayAsInput:pwName
pathway_species	getPathwayAsInput:pwSpecies
revision	getPathwayAsInput:revision
concat_filetype:output	writeFile:fileName
concat_filetype:output	writtenFile
getPathwayAsOutput:data	writeFile:data

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Thomask...

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Thomaskelder

Information Attributions (0)

(Workflows/Files)

None

[ edit ]

Information Tags (5)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

WikiPathways workflows

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3460 viewings

2303 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Write pathway to disk

Created by Thomaskelder on Tuesday 16 September 2008 11:20:54 (UTC)

Last edited by Thomaskelder on Tuesday 16 September 2008 11:35:55 (UTC)
Write pathway to disk

Created by Thomaskelder on Friday 14 November 2008 14:21:12 (UTC)

Revision comment:

Adapted workflow to stable identifiers on WikiPathways

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (2)

Taverna 1

Uploader

Thomask...

Get pathways by external reference (3)

Download

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.

Created: 2010-01-13

Credits: Thomaskelder

Taverna 2

Uploader

Thomask...

Download pathways for external references ... (2)

Download

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.

Created: 2009-02-03

Credits: Thomaskelder