BlatBlastCombi
Created: 2009-02-03 08:20:43
Last updated: 2009-02-03 08:28:06
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
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Workflow Components
Inputs (2)
| Name |
Description |
| DataBaseName |
|
| Sequences |
|
Processors (10)
| Name |
Type |
Description |
| Create_Sequence_Chunks |
beanshell |
|
| Flatten_list |
local |
|
| Split_sequences |
beanshell |
|
| Merge_string_list_to_string |
local |
|
| Chunk_Size |
stringconstant |
|
| Merge_string_list_to_string1 |
local |
|
| Write_Text_File |
local |
|
| Write_Text_File1 |
local |
|
| DoBioMart |
workflow |
|
| BlatOrBlast |
workflow |
|
Beanshells (10)
| Name |
Description |
Inputs |
Outputs |
| isRunning |
|
status
|
isRunning
|
| Correct_Moby_Object |
|
inputXML
|
outputXML
|
| 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
|
| EmptyList |
|
|
list
|
| Join_Blat_Blast_Results |
|
list1
list2
|
outputList
|
| isEmpty |
|
string
|
isEmpty
|
| Filter_Sequences_For_Blast |
|
sequences
blatResult
|
sequencesForBlast
|
| Create_Sequence_Chunks |
|
sequences
chunkSize
|
chunks
|
| Split_sequences |
|
sequenceText
|
sequences
|
Outputs (2)
| Name |
Description |
| Alignments |
|
| BioMartRecord |
|
Links (13)
| Source |
Sink |
| DataBaseName |
BlatOrBlast:DataBaseName |
| Sequences |
Split_sequences:sequenceText |
| BlatOrBlast:Alignments |
Flatten_list:inputlist |
| Chunk_Size:value |
Create_Sequence_Chunks:chunkSize |
| Create_Sequence_Chunks:chunks |
BlatOrBlast:Sequences |
| DoBioMart:records |
Merge_string_list_to_string1:stringlist |
| DoBioMart:records |
BioMartRecord |
| Flatten_list:outputlist |
Alignments |
| Flatten_list:outputlist |
DoBioMart:blastRecord |
| Flatten_list:outputlist |
Merge_string_list_to_string:stringlist |
| Merge_string_list_to_string1:concatenated |
Write_Text_File1:filecontents |
| Merge_string_list_to_string:concatenated |
Write_Text_File:filecontents |
| Split_sequences:sequences |
Create_Sequence_Chunks:sequences |
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licensed under:
Version 1 (earliest)
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