net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker
staph_strains.fna
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
blastall
net.sourceforge.taverna.scuflworkers.io.LocalCommand
C:\taverna-1.7.1\fasta.fna
net.sourceforge.taverna.scuflworkers.io.TextFileReader
\n
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
formatdb
net.sourceforge.taverna.scuflworkers.io.LocalCommand
C:\Program Files\ClustalW2\clustalw2
C:\taverna-1.7.1\fasta.fna
net.sourceforge.taverna.scuflworkers.io.LocalCommand
org.embl.ebi.escience.scuflworkers.java.StringListMerge
List cmdArgsList = new ArrayList();
cmdArgsList.add("-i");
cmdArgsList.add("./set7.fna");
cmdArgsList.add("-p");
cmdArgsList.add("tblastn");
cmdArgsList.add("-d");
cmdArgsList.add("customBLASTdb");
cmdArgsList.add("-o");
cmdArgsList.add("./blastReport");
cmdArgsList
This beanshell will not be run until after the fasta file is written from the Write_Fasta_File processor.
This beanshell creates an array of strings (a list of plain text), with each element containing one element of the arguments for the formatdb command line. Note that you can change the text in the beanshell in the element in the line after the one containing "-n" to set the name of the blast database you want.
If you want to add any other command line arguments, follow the system in the beanshell. E.g. add the flag, e.g. "-x" in one line, and its argument "somethingOrOther" in another line.
List cmdArgsList = new ArrayList();
cmdArgsList.add("-i");
cmdArgsList.add("./staph_strains.fna");
cmdArgsList.add("-p");
cmdArgsList.add("F");
cmdArgsList.add("-n");
cmdArgsList.add("customBLASTdb");
cmdArgsList
C:\taverna-1.7.1\blastReport
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
http://localhost:9000/SeqService?wsdl
getNeighbours
http://localhost:9000/SeqService?wsdl
addSequenceToFasta
http://localhost:9000/SeqService?wsdl
getSequences
file:/C:/taverna-1.7.1/isMRSA.xml
david.fox1@ncl.ac.uk
http://www.myexperiment.org/workflows/222/download?version=1
C:\Program Files\Rod Page\TreeView\treev32
C:\taverna-1.7.1\fasta.dnd
net.sourceforge.taverna.scuflworkers.io.LocalCommand
Completed
Write_Text_File
create_formatdb_cmdArgs
Scheduled
Running
Completed
local_create_blastdb
run_blastall
Scheduled
Running
Completed
run_blastall
parametersXML2
Scheduled
Running
Completed
getSequences
Read_FASTA
Scheduled
Running
Completed
addSequenceToFasta
Read_FASTA
Scheduled
Running
Completed
run_blastall
addSequenceToFasta
Scheduled
Running
Completed
run_blastall
getNeighbours
Scheduled
Running
Completed
Read_FASTA
ClustalW
Scheduled
Running
Completed
ClustalW
draw_tree
Scheduled
Running