Blat against ENSEMBLE Danio_rerio_Genome
Created: 2008-10-15 09:25:43
Last updated: 2008-10-15 09:27:23
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.
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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 |
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