Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[jabaws.git] / conf / settings / RNAalifoldOptionsOnly.xml

diff --git a/conf/settings/RNAalifoldOptionsOnly.xml b/conf/settings/RNAalifoldOptionsOnly.xml
new file mode 100644 (file)
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+++ b/conf/settings/RNAalifoldOptionsOnly.xml
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<runnerConfig>
+       <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
+       <options isRequired='false'>
+               <name>Endgaps</name>
+               <description>Score pairs with endgaps same as gap-gap pairs</description>
+               <optionNames>-E</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>Most Informative Sequence</name>
+               <description>Ouput Set of nucleotides with frequency > average</description>
+               <optionNames>--mis</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>Partition Function</name>
+               <description>Output partition function and probability matrix</description>
+               <optionNames>-p</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>Circular</name>
+               <description>Assume circular RNA molecule</description>
+               <optionNames>-c</optionNames>
+       </options>
+       <!--  Not Currently available with circular structures (-c) -->
+       <options isRequired='false'>
+               <name>G-Quadruplex</name>
+               <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
+               <optionNames>-g</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>d2</name>
+               <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
+               <optionNames>-d2</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>No LP</name>
+               <description>Produce Structures without lonely pairs</description>
+               <optionNames>--noLP</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>No GU</name>
+               <description>Do not allow GU pairs</description>
+               <optionNames>--noGU</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>No Closing GU</name>
+               <description>Do not allow GU pairs at the end of sequences</description>
+               <optionNames>--noClosingGU</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>old</name>
+               <description>Use old energy evaluation, treating gaps as characters</description>
+               <optionNames>--old</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>Ribosum Scoring</name>
+               <description>Use Ribosum Scoring Matrix</description>
+               <optionNames>-r</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>d2</name>
+               <description>
+               Dangling energies are added for the bases adjacent to a helix on both sides
+               </description>
+               <optionNames>-d2</optionNames>
+       </options>
+       <options isRequired='false'>
+               <name>MEA Structure</name>
+               <description>Maximum Expected Accuracy Structure</description>
+               <optionNames>--MEA</optionNames>
+       </options>
+       
+       
+       
+</runnerConfig>
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