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.

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http://myexperiment.org/workflows/392/download?version=1
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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)

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Information Tags (5)

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Information Shared with Groups (0)

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Information Featured In Packs (1)

WikiPathways workflows

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Information Attributed By (0)

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Information Favourited By (0)

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Information Statistics

3460 viewings

2303 downloads

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Citations (0)

None

Version History

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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

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