X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2Fsettings%2FRNAalifoldParameters.xml;h=a234019ecf374712a9f62e24ea82d9d9e7844d13;hb=0f73a668ad9aa4905b4c90948af0ede97b544c90;hp=b0e8df0ae89cd9c70a26d00fb951330eb9355612;hpb=424e935319103a35bea321a15911ad51fc78ebaf;p=jabaws.git

diff --git a/conf/settings/RNAalifoldParameters.xml b/conf/settings/RNAalifoldParameters.xml
index b0e8df0..a234019 100644
--- a/conf/settings/RNAalifoldParameters.xml
+++ b/conf/settings/RNAalifoldParameters.xml
@@ -5,8 +5,6 @@
 		<name>Endgaps</name>
 		<description>Score pairs with endgaps same as gap-gap pairs</description>
 		<optionNames>-E</optionNames>
-		<optionNames>--endgaps</optionNames>
-		<defaultValue>-E</defaultValue>
 	</options>
 	<options isRequired='false'>
 		<name>Most Informative Sequence</name>
@@ -19,42 +17,18 @@
 		<optionNames>-p</optionNames>
 	</options>
 	<options isRequired='false'>
-		<name>color</name>
-		<description>Consensus structure plot is colored</description>
-		<optionNames>--color</optionNames>
-	</options>
-	<options isRequired='false'>
-		<name>Alignment</name>
-		<description>Output structure annotated alignment</description>
-		<optionNames>--aln</optionNames>
-	</options>
-	<options isRequired='false'>
-		<name>No Postscript</name>	
-		<description>Do not produce postscript output</description>
-		<optionNames>--noPS</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>
-		<optionNames>--circ</optionNames>
-		<defaultValue>-c</defaultValue>
 	</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>
-		<optionNames>--gquad</optionNames>
-		<defaultValue>-g</defaultValue>
 	</options>
 	<options isRequired='false'>
-		<name>Dangling End Preset</name>
+		<name>d2</name>
 		<description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
 		<optionNames>-d2</optionNames>
 	</options>
@@ -82,95 +56,65 @@
 		<name>Ribosum Scoring</name>
 		<description>Use Ribosum Scoring Matrix</description>
 		<optionNames>-r</optionNames>
-		<optionNames>--ribosum_scoring</optionNames>
-		<defaultValue>-r</defaultValue>
 	</options>
-<!-- Constraints are entered on the command line followed by the input .aln file
-	 Causing problems for a batch RNAalifold execution system -->
-<!--  
-	<option isRequired='false'>
-		<name>Constraints</name>
-		<description>Structures calculated subject to constraints</description>
-		<optionNames>-C</optionNames>
-		<validValue>
-			<type>String</type>
-		</validValue>
-	</option> -->
-	<parameters isRequired='false'>
-		<name>MEA structure</name>
+	<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>
-		<defaultValue>1</defaultValue>
-		<validValue>
-			<type>Float</type>
-		</validValue>
-	</parameters>
-<!--  ?Will Jabaws recognize that arguments for the following params must
-be of the form -s INT and &dash-stochBT=INT -->
-	<parameters isRequired='false'>
-		<name>Stochastic Backtrack</name>
-		<description>Compute a number of random structures</description>
-		<optionNames>-s</optionNames>
-		<!-- Having multiple optionNames requires a default value but
-			in a parameter defaultValue refers to the argument -->
-<!-- 		<optionNames>-stochBT</optionNames> -->
-		<defaultValue>5</defaultValue>	<!-- arbitrary -->
-		<validValue>
-			<type>Int</type>
-		</validValue>
-	</parameters>
-	<parameters isRequired='false'>
-		<name>stochBT_en</name>
-		<description>Print Backtrack structures</description>
-		<optionNames>--stochBT_en</optionNames>
-		<defaultValue>5</defaultValue>  <!-- arbitrary -->
-		<validValue>
-			<type>Int</type>
-		</validValue>
-	</parameters>
+	</options>
+	
+	<prmSeparator> </prmSeparator>	
+	
 	<parameters isRequired='false'>
 		<name>scaling factor</name>
 		<description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
 		<optionNames>-S</optionNames>
-<!-- 		<optionNames>-pfScale</optionNames> -->
 		<defaultValue>1.07</defaultValue>
 		<validValue>
 			<type>Float</type>
+			<min>0</min>
+			<max>10</max>
 		</validValue>
 	</parameters>
 	<parameters isRequired='false'>
 		<name>bppmThreshold</name>
 		<description>Threshold for base pair probabilities</description>
 		<optionNames>--bppmThreshold</optionNames>
-		<defaultValue>1e-6</defaultValue>
+		<defaultValue>0.000001</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>0.00000001</min>
+			<max>1.0</max>
+		</validValue>
 	</parameters>
 	<parameters isRequired='false'>
 		<name>Temperature</name>
 		<description>Rescale Energy parameterss to Temperature</description>
 		<optionNames>-T</optionNames>
-<!-- 		<optionNames>-temp</optionNames> -->
 		<defaultValue>37</defaultValue>
 		<validValue>
-			<type>Double</type>
-		</validValue>
-	</parameters>
-	<parameters isRequired='false'>
-		<name>Dangling End</name>
-		<description>How to treat Dangling End energies for bases adjacent to helices</description>
-		<optionNames>-d</optionNames>
-<!-- 		<optionNames>-dangles</optionNames> -->
-		<defaultValue>2</defaultValue>
-		<validValue>
-			<type>Int</type>
+			<type>Float</type>
+			<min>-274</min>
+			<max>5000</max>
 		</validValue>
 	</parameters>
+	
 	<parameters isRequired='false'>
 		<name>cfactor</name>
 		<description>weight of covariance term</description>
 		<optionNames>--cfactor</optionNames>
 		<defaultValue>1.0</defaultValue>
 		<validValue>
-			<type>Double</type>
+			<type>Float</type>
+			<min>0</min>
+			<max>100</max>
 		</validValue>
 	</parameters>
 	<parameters isRequired='false'>
@@ -179,43 +123,10 @@ be of the form -s INT and &dash-stochBT=INT -->
 		<optionNames>--nfactor</optionNames>
 		<defaultValue>1.0</defaultValue>
 		<validValue>
-			<type>Double</type>
+			<type>Float</type>
+			<min>0</min>
+			<max>100</max>
 		</validValue>
 	</parameters>
 	
-<!-- 	 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> --> <!-- commentx2 -->
-<!-- 	</parameters> -->
-<!-- 	<parameters isRequired='false'> -->
-<!-- 		<name>Paramfile</name> -->
-<!-- 		<description>Use Energy parameters from a file</description> -->
-<!-- 		<optionNames>-P</optionNames> -->
-<!-- 		<optionNames>-paramFile</optionNames> --> <!-- commentx2 -->
-<!-- 		<validValue> -->
-<!-- 			<type>String</type> -->
-<!-- 		</validValue> -->
-<!-- 	</parameters> -->
-	
-	<parameters isRequired='false'>
-		<name>Allow Pairs</name>
-		<descrition>allow pairs in addition to AU, GC and GU</descrition>
-		<optionNames>--nsp</optionNames>
-		<defaultValue>-GA</defaultValue>
-		<validValue>
-			<type>String</type>
-		</validValue>
-	</parameters>
-	<parameters isRequired='false'>
-		<name>betaScale</name>
-		<description>Set scaling of Boltzmann factors</description>
-		<optionNames>--betaScale</optionNames>
-		<defaultValue>1.0</defaultValue>
-		<validValue>
-			<type>Double</type>
-		</validValue>
-	</parameters>
 </runnerConfig>
\ No newline at end of file