Workflow Entry: Download pathways for external references list

Created at: 14/11/08 @ 14:38:31

Version 2 (latest) (of 2)

Version created on: 14/11/08 @ 14:38:31 by: Thomaskelder | Revision comments Expand

Title: Download pathways for external references list

Type: Taverna 1

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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.

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/393/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (3)

Name	Description
xreflist	The location of a text file containing on each line a gene/protein/metabolite identifier (e.g. P04637).
output_path	The path to write the downloaded pathway files to.
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)

Processors (8)

Name	Type	Description
createFileName	beanshell
createPath	beanshell
count	beanshell
readXrefList	local
splitLines	local
clone_list	workflow
write_pathway	workflow
find_pathways_by_xref	workflow

Beanshells (3)

Name	Inputs	Outputs
createFileName	pathway_name path_name pathway_species	file_name
createPath	output_path xref	path_name
count	list	count

Outputs (1)

Name	Description
written_files	A list of files that were written.

Links (15)

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