Download pathways for external references list

Created: 2008-11-14 14:38:31

Download Workflow

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. An example of an input file containing a list of protein references can be found here.

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http://myexperiment.org/workflows/393/download?version=1
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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
splitLines	local
count	beanshell
createPath	beanshell
createFileName	beanshell
readXrefList	local
clone_list	workflow
find_pathways_by_xref	workflow
write_pathway	workflow

Beanshells (3)

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

Outputs (1)

Name	Description
written_files	A list of files that were written.

Links (16)

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_names	count:list
find_pathways_by_xref:pathway_names	createFileName:pathway_name
find_pathways_by_xref:pathway_names	write_pathway:pathway_name
find_pathways_by_xref:pathway_species	createFileName:pathway_species
find_pathways_by_xref:pathway_species	write_pathway:pathway_species
readXrefList:filecontents	splitLines:string
splitLines:split	createPath:xref
splitLines:split	find_pathways_by_xref:identifier
write_pathway:writtenFile	written_files

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 (1)

(Workflows/Files)

CloneItemsInList

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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 Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3099 viewings

2166 downloads

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Citations (0)

None

Version History

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Download pathways for external references list

Created by Thomaskelder on Tuesday 16 September 2008 11:32:47 (UTC)

Last edited by Thomaskelder on Tuesday 16 September 2008 11:41:39 (UTC)
Download pathways for external references list

Created by Thomaskelder on Friday 14 November 2008 14:38:31 (UTC)

Revision comment:

Adapted workflow to stable identifiers on WikiPathways

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