1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
2 <runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3 xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
4 <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
5 <options isRequired='false'>
7 <description>Score pairs with endgaps same as gap-gap pairs</description>
8 <optionNames>-E</optionNames>
9 <optionNames>--endgaps</optionNames>
10 <defaultValue>-E</defaultValue>
12 <options isRequired='false'>
13 <name>Most Informative Sequence</name>
14 <description>Ouput Set of nucleotides with frequency > average</description>
15 <optionNames>--mis</optionNames>
17 <options isRequired='false'>
18 <name>Partition Function</name>
19 <description>Output partition function and probability matrix</description>
20 <optionNames>-p</optionNames>
21 <optionNames>--partfunc</optionNames>
22 <defaultValue>-p</defaultValue>
24 <options isRequired='false'>
26 <description>deactivates the calculation of the pair probabilities</description>
27 <optionNames>-p0</optionNames>
29 <options isRequired='false'>
31 <description>Consensus structure plot is colored</description>
32 <optionNames>--color</optionNames>
34 <options isRequired='false'>
35 <name>Alignment</name>
36 <description>Output structure annotated alignment</description>
37 <optionNames>--aln</optionNames>
39 <options isRequired='false'>
40 <name>No Postscript</name>
41 <description>Do not produce postscript output</description>
42 <optionNames>--noPS</optionNames>
44 <options isRequired='false'>
46 <description>Assume circular RNA molecule</description>
47 <optionNames>-c</optionNames>
48 <optionNames>--circ</optionNames>
49 <defaultValue>-c</defaultValue>
51 <!-- Not Currently available with circular structures (-c) -->
52 <options isRequired='false'>
53 <name>G-Quadruplex</name>
54 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
55 <optionNames>-g</optionNames>
56 <optionNames>--gquad</optionNames>
57 <defaultValue>-g</defaultValue>
59 <options isRequired='false'>
61 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
62 <optionNames>-d2</optionNames>
64 <options isRequired='false'>
66 <description>Produce Structures without lonely pairs</description>
67 <optionNames>--noLP</optionNames>
69 <options isRequired='false'>
71 <description>Do not allow GU pairs</description>
72 <optionNames>--noGU</optionNames>
74 <options isRequired='false'>
75 <name>No Closing GU</name>
76 <description>Do not allow GU pairs at the end of sequences</description>
77 <optionNames>--noClosingGU</optionNames>
79 <options isRequired='false'>
81 <description>Use old energy evaluation, treating gaps as characters</description>
82 <optionNames>--old</optionNames>
84 <options isRequired='false'>
85 <name>Ribosum Scoring</name>
86 <description>Use Ribosum Scoring Matrix</description>
87 <optionNames>-r</optionNames>
88 <optionNames>--ribosum_scoring</optionNames>
89 <defaultValue>-r</defaultValue>
91 <options isRequired='false'>
94 Dangling energies are added for the bases adjacent to a helix on both sides
96 <optionNames>-d2</optionNames>
98 <options isRequired='false'>
99 <name>MEA Structure</name>
100 <description>Maximum Expected Accuracy Structure</description>
101 <optionNames>--MEA</optionNames>
103 <!-- Constraints are entered on the command line followed by the input .aln file
104 Causing problems for a batch RNAalifold execution system -->
106 <option isRequired='false'>
107 <name>Constraints</name>
108 <description>Structures calculated subject to constraints</description>
109 <optionNames>-C</optionNames>
115 <prmSeparator> </prmSeparator>
116 <parameters isRequired='false'>
117 <name>Stochastic Backtrack</name>
118 <description>Compute a number of random structures</description>
119 <optionNames>-s</optionNames>
120 <!-- Having multiple optionNames requires a default value but -->
121 <!-- in a parameter defaultValue refers to the argument -->
122 <!-- <optionNames>-stochBT</optionNames> -->
123 <defaultValue>5</defaultValue>
130 <parameters isRequired='false'>
131 <name>stochBT_en</name>
132 <description>Print Backtrack structures</description>
133 <optionNames>--stochBT_en</optionNames>
134 <defaultValue>5</defaultValue> <!-- arbitrary -->
141 <parameters isRequired='false'>
142 <name>scaling factor</name>
143 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
144 <optionNames>-S</optionNames>
145 <!-- <optionNames>-pfScale</optionNames> -->
146 <defaultValue>1.07</defaultValue>
153 <parameters isRequired='false'>
154 <name>bppmThreshold</name>
155 <description>Threshold for base pair probabilities</description>
156 <optionNames>--bppmThreshold</optionNames>
157 <defaultValue>0.000001</defaultValue>
160 <min>0.0000000000001</min>
164 <parameters isRequired='false'>
165 <name>Temperature</name>
166 <description>Rescale Energy parameterss to Temperature</description>
167 <optionNames>-T</optionNames>
168 <!-- <optionNames>-temp</optionNames> -->
169 <defaultValue>37</defaultValue>
176 <parameters isRequired='false'>
177 <name>Dangling End</name>
178 <description>How to treat Dangling End energies for bases adjacent to helices</description>
179 <optionNames>-d</optionNames>
180 <!-- <optionNames>-dangles</optionNames> -->
181 <defaultValue>2</defaultValue>
188 <parameters isRequired='false'>
190 <description>weight of covariance term</description>
191 <optionNames>--cfactor</optionNames>
192 <defaultValue>1.0</defaultValue>
199 <parameters isRequired='false'>
201 <description>penalty for non-compatible sequences in covariance term</description>
202 <optionNames>--nfactor</optionNames>
203 <defaultValue>1.0</defaultValue>
211 <!-- How to deal with default/possible values for parameter files? -->
212 <!-- <parameters isRequired='false'> -->
213 <!-- <name>Ribosum File</name> -->
214 <!-- <description>Use Specified Ribosum Matrix</description> -->
215 <!-- <optionNames>-R</optionNames> -->
216 <!-- <optionNames>-ribosum_file</optionNames> -->
217 <!-- </parameters> -->
218 <!-- <parameters isRequired='false'> -->
219 <!-- <name>Paramfile</name> -->
220 <!-- <description>Use Energy parameters from a file</description> -->
221 <!-- <optionNames>-P</optionNames> -->
222 <!-- <optionNames>-paramFile</optionNames> -->
223 <!-- <validValue> -->
224 <!-- <type>String</type> -->
225 <!-- </validValue> -->
226 <!-- </parameters> -->
228 <!-- The values of this parameter are in the form of a comma separated
229 list of allowed pairs. This makes a complete parameter list
230 too large to be represented as a list of possible values
231 How to deal with this? -->
232 <!-- just support the most biologically viable pairs? -->
234 <parameters isRequired='false'>
235 <name>Allow Pairs</name>
236 <description>allow pairs in addition to AU, GC and GU</description>
237 <optionNames>--nsp</optionNames>
238 <defaultValue>-GA</defaultValue>
239 <possibleValues>-GA</possibleValues>
240 <possibleValues>-AG</possibleValues>
242 <!-- Is dependant on -p (partfunc) -->
243 <parameters isRequired='false'>
244 <name>betaScale</name>
245 <description>Set scaling of Boltzmann factors</description>
246 <optionNames>--betaScale</optionNames>
247 <defaultValue>1.0</defaultValue>