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Write pathway to disk

Workflow Entry: Write pathway to disk

Created at: 14/11/08 @ 14:21:12 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	See the Service entry for this web service.
getPathwayAs_input	local

Beanshells (1)

Name	Description	Inputs	Outputs
writeFile		data fileName

Outputs (1)

Name	Description
writtenFile	The file that was written.

Links (11)

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

Coordinations (0)

Information Workflow Type

Taverna 1

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

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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)

Current:

0.0 / 5

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Information Attributed By (0)

(Workflows/Files)

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Information Favourited By (0)

No one

Information Statistics

607 viewings

929 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Write pathway to disk

Created on: Tuesday 16 September 2008 @ 11:20:54 (GMT)

Created by: Thomaskelder

Last edited on: Tuesday 16 September 2008 @ 11:35:55 (GMT)

Last edited by: Thomaskelder

Revision comments:

None

Latest Version:
[2] - Write pathway to disk

Created on: Friday 14 November 2008 @ 14:21:12 (GMT)

Created by: Thomaskelder

Revision comments:

Adapted workflow to stable identifiers on WikiPathways

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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):

View

Download (v3)

Taverna 2

Original Uploader

Thomask...

Download pathways for external references list (Taverna 2) (v1)

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

Credits: Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 108 times | Downloaded: 51 times

Tags (5):