<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>
<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>
<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'>
<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
git://source.jalview.org / jabaws.git / blobdiff