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