this is the comand processor to invoke the treeview software and display the phylip tree which generated by clustalw
C:\Program Files\Rod Page\TreeView\treev32
C:\clustalw\pro_clustalw.dnd
net.sourceforge.taverna.scuflworkers.io.LocalCommand
c:\clustalw\pro_clustalw.fna
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
This processor is the local java code to parse the mecA gene from the EMBL file.
http://wheel94:9000/SeqService?wsdl
mecASearch
this is a local processor that recongnize the best hit of the blast result.
http://wheel94:9000/SeqService?wsdl
strainRecognizer
This retreive the protein sequence and generate as FASTA file
net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker
This work flow is a simple comand of clustalw. To make it run , you need to install clastalw to you local machine.
This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from).
Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.
Shortcomings:
The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.
All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use.
This runs the blastall command (NCBI blast) on your local machine. This means you need to have blastall installed. The location provided is /usr/local/bin/blastall, so if your executable is not in that location, you will need to edit this. If you are working on a Bio-Linux machine, this should work for you without change.
Note that the blast results are written to your hard disk in the working directory by default. Edit the location indicated in the create_blastall_cmdArgs beanshell in the line after the one adding "-o" if you are not happy with this.
c:\clustalw\clustalw
c:\clustalw\pro_clustalw.fna
net.sourceforge.taverna.scuflworkers.io.LocalCommand
retrieve the emble file based on the strainX url
http://www.ebi.ac.uk/cgi-bin/dbfetch?db=embl&style=raw&id=AJ938182
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
This nested workflow is from my experiment. using fetchBatch to retreive a list of sequence
uniprot
file:/C:/Taverna-1.7.1/taverna-1.7.1/teambest/EBI_dbfetch_fetchBatch(good).xml
This workflow is using local blast and local database to get the blast result of query sequence
file:/C:/Taverna-1.7.1/taverna-1.7.1/teambest/Genome_Blast(No.2).xml
This Nested workflow is come from my experiment. thanks the author here.
Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params.
uniprot
hagn@ee.com
blastp
Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params.
List of input data items for the job. In the case of WU-BLAST this is a list containing one input sequence.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Pack the input sequence into the structure required.
sequence
uniprot:wap_rat
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Unpack the byte[] into a string for display.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the list of hit identifiers from the job.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsdl
getIds
Get the XML result for the job.
toolxml
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsdl
poll
Submit the WU-BLAST job.
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsdl
runWUBlast
Parameters for the WU-BLAST job.
1. Expectation threshold set to 0.00001
2. Maximum number of hit reported set to 10.
blastp
uniprot
0.00001
10
10
1
your@email
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Check if job has completed.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/wublast#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsdl
checkStatus
The name of the database to search (e.g. uniprot).
Your e-mail address.
The BLAST program to use for the search (e.g. blastp).
List of the identifers of the hits found by the search.
application/octet-stream
XML version of the BLAST output.
Identifier of the job run.
Completed
Poll_Job
Get_XML_Result
Scheduled
Running
Completed
Poll_Job
Get_Hit_ID_List
Scheduled
Running
Using housekeep gene code protein as parameter to build the phylip tree.
image/png
image/gif
Completed
Write_Text_File
run_Clustalw
Scheduled
Running
Completed
run_Clustalw
Tree_View
Scheduled
Running