Workflow Entry: Blat against ENSEMBLE Danio_rerio_Genome

Created at: 15/10/08 @ 09:25:43 Last updated: 15/10/08 @ 09:27:23

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Version created on: 15/10/08 @ 09:25:43 by: Wassinki | Revision comments Expand

Last edited on: 15/10/08 @ 09:27:24 by: Wassinki

Title: Blat against ENSEMBLE Danio_rerio_Genome

Type: Taverna 1

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Description

The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value.

To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to install this certificate.

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/532/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
DataBase	Database name (Danio_rerio_Genome for Zebra Fish)
Sequences	Sequences in fasta format

Processors (12)

Name	Type	Description
Flatten_urls	local
Download_Report_and_Filter	beanshell	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.
eValue	stringconstant
Parse_Moby_Data_URL	biomobyparser	Processor to parse the datatype URL
MobyBlat	biomobywsdl	BioMOBY web service wrapper for the command line query tool 'BLAT'.
Email	biomobyobject	An e-mail address object.
BlatJob	biomobyobject	A BLAT job.
DataBase	biomobyobject	A database object.
User	biomobyobject	A generic user object.
FASTA	biomobyobject	FASTA formatted sequence
String	biomobyobject	a string
Password	biomobyobject	A generic password object.

Beanshells (1)

Name	Description	Inputs	Outputs
Download_Report_and_Filter	This Beanshell downloads a file to disk. The standard download local Java widgets don't handle URLs with HTTP(S) Basic Authentication, but this Beanshell can. When a webserver uses BasicAuth, a login and password can be coded as part of the URL using the following syntax: http(s)://login:password@www.some.website/my/great/tool/result.xml. This beanshel extracts the login and password from the URL and supplies them automatically to the webserver. This prevents Taverna from showing popup dialogs requesting the login and password from the user as this will be problematic for large workflows. Please note that the path where the downloaded file will be stored must be an absolute path to a folder ended with a slash. (Slash backward on Windows or a slash forward on Linux/Unix/Mac OS X.) The filename for the result is automatically extracted from the URL.	URL eValue	blatResults

Outputs (1)

Name	Description
blatResults

Links (14)

Source	Sink
BlatJob:mobyData	MobyBlat:BlatJob(input)
DataBase	DataBase:id
DataBase:mobyData	BlatJob:DataBase(database)
Email:mobyData	User:Email(email)
FASTA:mobyData	BlatJob:FASTA(fasta)
MobyBlat:URL(result)	Parse_Moby_Data_URL:mobyData('URL')
Sequences	String:value
Download_Report_and_Filter:blatResults	blatResults
Flatten_urls:concatenated	Download_Report_and_Filter:URL
Parse_Moby_Data_URL:id	Flatten_urls:stringlist
Password:mobyData	User:Password(password)
String:mobyData	FASTA:String(content)
User:mobyData	MobyBlat:User(user)
eValue:value	Download_Report_and_Filter:eValue