Hi Peter, Thanks for your quick reply!
That makes perfect sense. Joni On Mon, Nov 7, 2011 at 10:40 AM, Peter Troshin <[email protected]>wrote: > Hi Joni, > > The "Option" is a single value whereas the "Parameter" is a key value > pair. > For example option: > <options> > <name>No transition weighting</name> > <description>Disable sequence weighting</description> > <optionNames>-NOWEIGHTS</optionNames> > </options> > > Will be converted by JABAWS to the command line option: -NOWEIGHTS > > While the parameter: > <parameters> > <name>Transition weighting</name> > <description>Type of the sequence (PROTEIN or DNA)</description> > <optionNames>-TRANSWEIGHT</optionNames> > <furtherDetails>prog_docs/clustalw.txt</furtherDetails> > <defaultValue>0.5</defaultValue> > <validValue> > <type>Float</type> > <min>0</min> > <max>10</max> > </validValue> > </parameters> > 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: > <prmSeparator>=</prmSeparator> > > 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 <options> > nodes and <parameters> 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 > > > _______________________________________________ > Jalview-discuss mailing > [email protected]http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > > > -- Plant and Computational Genomics Group Joint Genome Institute - U.S. Dept. of Energy http://www.phytozome.net
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