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>
21 <options isRequired='false'>
23 <description>Consensus structure plot is colored</description>
24 <optionNames>--color</optionNames>
26 <options isRequired='false'>
27 <name>Alignment</name>
28 <description>Output structure annotated alignment</description>
29 <optionNames>--aln</optionNames>
31 <options isRequired='false'>
32 <name>No Postscript</name>
33 <description>Do not produce postscript output</description>
34 <optionNames>--noPS</optionNames>
36 <options isRequired='false'>
37 <name>Partition Function</name>
38 <description>Output partition function and probability matrix</description>
39 <optionNames>-p</optionNames>
41 <options isRequired='false'>
43 <description>Assume circular RNA molecule</description>
44 <optionNames>-c</optionNames>
45 <optionNames>--circ</optionNames>
46 <defaultValue>-c</defaultValue>
48 <!-- Not Currently available with circular structures (-c) -->
49 <options isRequired='false'>
50 <name>G-Quadruplex</name>
51 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
52 <optionNames>-g</optionNames>
53 <optionNames>--gquad</optionNames>
54 <defaultValue>-g</defaultValue>
56 <options isRequired='false'>
57 <name>Dangling End Preset</name>
58 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
59 <optionNames>-d2</optionNames>
61 <options isRequired='false'>
63 <description>Produce Structures without lonely pairs</description>
64 <optionNames>--noLP</optionNames>
66 <options isRequired='false'>
68 <description>Do not allow GU pairs</description>
69 <optionNames>--noGU</optionNames>
71 <options isRequired='false'>
72 <name>No Closing GU</name>
73 <description>Do not allow GU pairs at the end of sequences</description>
74 <optionNames>--noClosingGU</optionNames>
76 <options isRequired='false'>
78 <description>Use old energy evaluation, treating gaps as characters</description>
79 <optionNames>--old</optionNames>
81 <options isRequired='false'>
82 <name>Ribosum Scoring</name>
83 <description>Use Ribosum Scoring Matrix</description>
84 <optionNames>-r</optionNames>
85 <optionNames>--ribosum_scoring</optionNames>
86 <defaultValue>-r</defaultValue>
88 <!-- Constraints are entered on the command line followed by the input .aln file
89 Causing problems for a batch RNAalifold execution system -->
91 <option isRequired='false'>
92 <name>Constraints</name>
93 <description>Structures calculated subject to constraints</description>
94 <optionNames>-C</optionNames>
99 <parameters isRequired='false'>
100 <name>MEA structure</name>
101 <description>Maximum Expected Accuracy Structure</description>
102 <optionNames>--MEA</optionNames>
103 <defaultValue>1</defaultValue>
108 <!-- ?Will Jabaws recognize that arguments for the following params must
109 be of the form -s INT and &dash-stochBT=INT -->
110 <parameters isRequired='false'>
111 <name>Stochastic Backtrack</name>
112 <description>Compute a number of random structures</description>
113 <optionNames>-s</optionNames>
114 <!-- Having multiple optionNames requires a default value but
115 in a parameter defaultValue refers to the argument -->
116 <!-- <optionNames>-stochBT</optionNames> -->
117 <defaultValue>5</defaultValue> <!-- arbitrary -->
122 <parameters isRequired='false'>
123 <name>stochBT_en</name>
124 <description>Print Backtrack structures</description>
125 <optionNames>--stochBT_en</optionNames>
126 <defaultValue>5</defaultValue> <!-- arbitrary -->
131 <parameters isRequired='false'>
132 <name>scaling factor</name>
133 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
134 <optionNames>-S</optionNames>
135 <!-- <optionNames>-pfScale</optionNames> -->
136 <defaultValue>1.07</defaultValue>
141 <parameters isRequired='false'>
142 <name>bppmThreshold</name>
143 <description>Threshold for base pair probabilities</description>
144 <optionNames>--bppmThreshold</optionNames>
145 <defaultValue>1e-6</defaultValue>
147 <parameters isRequired='false'>
148 <name>Temperature</name>
149 <description>Rescale Energy parameterss to Temperature</description>
150 <optionNames>-T</optionNames>
151 <!-- <optionNames>-temp</optionNames> -->
152 <defaultValue>37</defaultValue>
157 <parameters isRequired='false'>
158 <name>Dangling End</name>
159 <description>How to treat Dangling End energies for bases adjacent to helices</description>
160 <optionNames>-d</optionNames>
161 <!-- <optionNames>-dangles</optionNames> -->
162 <defaultValue>2</defaultValue>
167 <parameters isRequired='false'>
169 <description>weight of covariance term</description>
170 <optionNames>--cfactor</optionNames>
171 <defaultValue>1.0</defaultValue>
176 <parameters isRequired='false'>
178 <description>penalty for non-compatible sequences in covariance term</description>
179 <optionNames>--nfactor</optionNames>
180 <defaultValue>1.0</defaultValue>
186 <!-- How to deal with default/possible values for parameter files? -->
187 <!-- <parameters isRequired='false'> -->
188 <!-- <name>Ribosum File</name> -->
189 <!-- <description>Use Specified Ribosum Matrix</description> -->
190 <!-- <optionNames>-R</optionNames> -->
191 <!-- <optionNames>-ribosum_file</optionNames> --> <!-- commentx2 -->
192 <!-- </parameters> -->
193 <!-- <parameters isRequired='false'> -->
194 <!-- <name>Paramfile</name> -->
195 <!-- <description>Use Energy parameters from a file</description> -->
196 <!-- <optionNames>-P</optionNames> -->
197 <!-- <optionNames>-paramFile</optionNames> --> <!-- commentx2 -->
198 <!-- <validValue> -->
199 <!-- <type>String</type> -->
200 <!-- </validValue> -->
201 <!-- </parameters> -->
203 <parameters isRequired='false'>
204 <name>Allow Pairs</name>
205 <descrition>allow pairs in addition to AU, GC and GU</descrition>
206 <optionNames>--nsp</optionNames>
207 <defaultValue>-GA</defaultValue>
212 <parameters isRequired='false'>
213 <name>betaScale</name>
214 <description>Set scaling of Boltzmann factors</description>
215 <optionNames>--betaScale</optionNames>
216 <defaultValue>1.0</defaultValue>