About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
Query caArray data service and retrieving files

Workflow Entry: Query caArray data service and retrieving files

Created at: 24/05/10 @ 22:55:57 Last updated: 24/05/10 @ 22:55:58

Version 2 (latest) (of 2)

Version created on: 24/05/10 @ 22:55:57 by: Wei Tan | Revision comments Expand

Title: Query caArray data service and retrieving files

Type: Taverna 2

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

need to install Taverna 2 caGrid integration suite from http://www.mcs.anl.gov/~wtan/t2/ and get a cagrid Dorian account (see http://wiki.cagrid.org/display/caGrid13/Home)

Download

Download Workflow File/Package (T2FLOW)

Download Workflow as a Galaxy tool

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1254/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (3)

Name	Description
experiment_id	experiment id in caArray database experiment id in caArray database. see https://array.nci.nih.gov/caarray/
resultFileName	the file name of the result to be downloaded
workingDir	the local directory to download the result file

Processors (9)

Name	Type	Description
createFileTransfer	activity
createFileTransfer_input	xmlsplitter
createFileTransfer_caArrayFile	xmlsplitter
createFileTransfer_output	xmlsplitter
createFileTransfer_TransferServiceContextReference	xmlsplitter
CaGrid_Transfer_Activity	transfer
CQL_Builder	cql
query	activity
extract_a_file	beanshell

Beanshells (1)

Name	Description	Inputs	Outputs
extract_a_file		caArrayFiles	caArrayFile

Outputs (1)

Name	Description
resultFile

Datalinks (12)

Source	Sink
createFileTransfer_input:output	createFileTransfer:parameters
createFileTransfer_caArrayFile:output	createFileTransfer_input:caArrayFile
extract_a_file:caArrayFile	createFileTransfer_caArrayFile:CaArrayFile
createFileTransfer:parameters	createFileTransfer_output:input
createFileTransfer_output:TransferServiceContextReference	createFileTransfer_TransferServiceContextReference:input
createFileTransfer_TransferServiceContextReference:EndpointReference	CaGrid_Transfer_Activity:epr
resultFileName	CaGrid_Transfer_Activity:fileName
workingDir	CaGrid_Transfer_Activity:workingDir
experiment_id	CQL_Builder:exp_id
CQL_Builder:value	query:parameters
query:parameters	extract_a_file:caArrayFiles
CaGrid_Transfer_Activity:fileName	resultFile

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Wei Tan

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Wei Tan

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Original Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

127 viewings

386 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Query caArray data service and retrieve files

Created on: Tuesday 11 May 2010 @ 20:11:56 (GMT)

Created by: Wei Tan

Last edited on: Tuesday 11 May 2010 @ 20:18:13 (GMT)

Last edited by: Wei Tan

Revision comments:

None

Latest Version:
[2] - Query caArray data service and retrieving files

Created on: Monday 24 May 2010 @ 22:55:57 (GMT)

Created by: Wei Tan

Revision comments:

None

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (1)

Taverna 2

Original Uploader

Wei Tan

A simple CQL query workflow in caGrid (v1)

Created: 24/05/10 @ 23:52:05 | Last updated: 25/05/10 @ 19:20:30

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

1. CQL is a language to query data from caGrid/caBIG services. This workflow is tested with Taverna 2.1.2 and the caGrid Workflow Suite downloadable from http://www.mcs.anl.gov/~wtan/t2/. 2.More information regarding CQL can be found from http://wiki.cagrid.org/display/dataservices. 3. Sample input (95) is provided in the workflow. It is to query all the hybridization data within a microarray experiment whose id is 95.

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

Viewed: 31 times | Downloaded: 10 times

Tags (5):