Hello,
I am working to add some additional msa tools to our jabaws installation. I have a question about the configuration files for my new services. What is the difference between an option and a parameter in a settings file? For example, in the ClustalParameters.xml file there are both nodes and nodes, but I’m not sure what the difference is.
Thanks,
Joni
···
–
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
Hi Joni,
The “Option” is a single value whereas the “Parameter” is a key value pair.
For example option:
No transition weighting
Disable sequence weighting
-NOWEIGHTS
Will be converted by JABAWS to the command line option: -NOWEIGHTS
While the parameter:
Transition weighting
Type of the sequence (PROTEIN or DNA)
-TRANSWEIGHT
prog_docs/clustalw.txt
0.5
Float
0
10
In the command line will look like this: -TRANSWEIGHT=0.5
if no value is specified by the user.
The actual delimiter between the parameter and the value is defined by the “prmSeparator” value, in this case it is defined like this: =
I hope that helps.
Regards,
Peter
Hi Peter,
Thanks for your quick reply!
That makes perfect sense.
Joni
···
On Mon, Nov 7, 2011 at 10:40 AM, Peter Troshin <p.v.troshin@dundee.ac.uk> wrote:
Hi Joni,
The “Option” is a single value whereas the “Parameter” is a key value pair.
For example option:
No transition weighting
Disable sequence weighting
-NOWEIGHTS
Will be converted by JABAWS to the command line option: -NOWEIGHTS
While the parameter:
Transition weighting
Type of the sequence (PROTEIN or DNA)
-TRANSWEIGHT
prog_docs/clustalw.txt
0.5
Float
0
10
In the command line will look like this: -TRANSWEIGHT=0.5
if no value is specified by the user.
The actual delimiter between the parameter and the value is defined by the “prmSeparator” value, in this case it is defined like this: =
I hope that helps.
Regards,
Peter
On 07/11/2011 18:20, Joni Fazo wrote:
Hello,
I am working to add some additional msa tools to our jabaws installation. I have a question about the configuration files for my new services. What is the difference between an option and a parameter in a settings file? For example, in the ClustalParameters.xml file there are both nodes and nodes, but I’m not sure what the difference is.
Thanks,
Joni
–
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
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–
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net