Workflow Entry: BlatBlastCombi

Created at: 03/02/09 @ 08:20:43 Last updated: 03/02/09 @ 08:28:06

Version 2 (latest) (of 2)

Version created on: 03/02/09 @ 08:20:43 by: Wassinki | Revision comments Expand

Last edited on: 03/02/09 @ 08:28:07 by: Wassinki

Title: BlatBlastCombi

Type: Taverna 1

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Description

This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.

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.

http://www.myexperiment.org/files/148

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/531/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
DataBaseName	The name of the database (Danio_rerio_Genome for Zebra Fish)
Sequences	Fasta sequences

Processors (8)

Name	Type	Description
Join_Blat_Blast_Results	beanshell
isEmpty	beanshell
Fail_if_true	local
EmptyList	beanshell
Fail_if_false	local
Filter_Sequences_For_Blast	beanshell
Blast	workflow	This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.
Blat	workflow	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.

Beanshells (8)

Name	Description	Inputs	Outputs
Correct_Moby_Object		inputXML	outputXML
isRunning		status	isRunning
DownloadURLWithBasicAuth	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.	theURL	blastResults
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
Join_Blat_Blast_Results		list1 list2	outputList
isEmpty		string	isEmpty
EmptyList			list
Filter_Sequences_For_Blast		sequences blatResult	sequencesForBlast

Outputs (1)

Name	Description
Alignments

Links (13)

Source	Sink
DataBaseName	Blast:DataBaseName
DataBaseName	Blat:DataBase
Sequences	Blat:Sequences
Sequences	Filter_Sequences_For_Blast:sequences
Blast:BlatResults	Join_Blat_Blast_Results:list2
Blat:blatResults	Filter_Sequences_For_Blast:blatResult
Blat:blatResults	Join_Blat_Blast_Results:list1
EmptyList:list	Join_Blat_Blast_Results:list2
Filter_Sequences_For_Blast:sequencesForBlast	Blast:Sequences
Filter_Sequences_For_Blast:sequencesForBlast	isEmpty:string
isEmpty:isEmpty	Fail_if_false:test
isEmpty:isEmpty	Fail_if_true:test
Join_Blat_Blast_Results:outputList	Alignments