-<!-- How to deal with default/possible values for parameter files? -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Ribosum File</name> -->
-<!-- <description>Use Specified Ribosum Matrix</description> -->
-<!-- <optionNames>-R</optionNames> -->
-<!-- <optionNames>-ribosum_file</optionNames> -->
-<!-- </parameters> -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Paramfile</name> -->
-<!-- <description>Use Energy parameters from a file</description> -->
-<!-- <optionNames>-P</optionNames> -->
-<!-- <optionNames>-paramFile</optionNames> -->
-<!-- <validValue> -->
-<!-- <type>String</type> -->
-<!-- </validValue> -->
-<!-- </parameters> -->
-
- <!-- The values of this parameter are in the form of a comma separated
- list of allowed pairs. This makes a complete parameter list
- too large to be represented as a list of possible values
- How to deal with this? -->
- <!-- just support the most biologically viable pairs? -->
-
- <parameters isRequired='false'>
- <name>Allow Pairs</name>
- <description>allow pairs in addition to AU, GC and GU</description>
- <optionNames>--nsp</optionNames>
- <defaultValue>-GA</defaultValue>
- <possibleValues>-GA</possibleValues>
- <possibleValues>-AG</possibleValues>
- </parameters>
- <!-- Is dependant on -p (partfunc) -->
- <parameters isRequired='false'>
- <name>betaScale</name>
- <description>Set scaling of Boltzmann factors</description>
- <optionNames>--betaScale</optionNames>
- <defaultValue>1.0</defaultValue>
- <validValue>
- <type>Float</type>
- <min>0</min>
- <max>100000</max>
- </validValue>
- </parameters>