Workflow Entry: Write pathway to disk

Created at: 16/09/08 @ 11:20:54 Last updated: 14/11/08 @ 14:21:13

Version 2 (latest) (of 2)

Version created on: 14/11/08 @ 14:21:12 by: Thomaskelder | Revision comments Expand

Title: Write pathway to disk

Type: Taverna 1

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Description

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

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/392/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (4)

Name	Description
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).
pathway_id

Processors (6)

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

Beanshells (1)

Name	Description	Inputs	Outputs
writeFile		data fileName

Outputs (1)

Name	Description
writtenFile	The file that was written.

Links (11)

Sink	Source
concat_dot:string1	file_name
concat_filetype:string1	concat_dot:output
concat_filetype:string2	file_type
writeFile:fileName	concat_filetype:output
getPathwayAs_input:fileType	file_type
writeFile:data	getPathwayAsOutput:data
getPathwayAs_input:pwId	pathway_id
getPathwayAs_input:revision	revision
getPathwayAsOutput:input	getPathwayAs:parameters
getPathwayAs:parameters	getPathwayAs_input:output
writtenFile	concat_filetype:output