conf/settings/RNAalifoldParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
   2 <runnerConfig>
   3         <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
   4         <options isRequired='false'>
   5                 <name>Endgaps</name>
   6                 <description>Score pairs with endgaps same as gap-gap pairs</description>
   7                 <optionNames>-E</optionNames>
   8                 <optionNames>--endgaps</optionNames>
   9                 <defaultValue>-E</defaultValue>
  10         </options>
  11         <options isRequired='false'>
  12                 <name>Most Informative Sequence</name>
  13                 <description>Ouput Set of nucleotides with frequency > average</description>
  14                 <optionNames>--mis</optionNames>
  15         </options>
  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>
  22         </options>
  23         <options isRequired='false'>
  24                 <name>p0</name>
  25                 <description>deactivates the calculation of the pair probabilities</description>
  26                 <optionNames>-p0</optionNames>
  27         </options>
  28         <options isRequired='false'>
  29                 <name>color</name>
  30                 <description>Consensus structure plot is colored</description>
  31                 <optionNames>--color</optionNames>
  32         </options>
  33         <options isRequired='false'>
  34                 <name>Alignment</name>
  35                 <description>Output structure annotated alignment</description>
  36                 <optionNames>--aln</optionNames>
  37         </options>
  38         <options isRequired='false'>
  39                 <name>No Postscript</name>
  40                 <description>Do not produce postscript output</description>
  41                 <optionNames>--noPS</optionNames>
  42         </options>
  43         <options isRequired='false'>
  44                 <name>Circular</name>
  45                 <description>Assume circular RNA molecule</description>
  46                 <optionNames>-c</optionNames>
  47                 <optionNames>--circ</optionNames>
  48                 <defaultValue>-c</defaultValue>
  49         </options>
  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>
  57         </options>
  58         <options isRequired='false'>
  59                 <name>d2</name>
  60                 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
  61                 <optionNames>-d2</optionNames>
  62         </options>
  63         <options isRequired='false'>
  64                 <name>No LP</name>
  65                 <description>Produce Structures without lonely pairs</description>
  66                 <optionNames>--noLP</optionNames>
  67         </options>
  68         <options isRequired='false'>
  69                 <name>No GU</name>
  70                 <description>Do not allow GU pairs</description>
  71                 <optionNames>--noGU</optionNames>
  72         </options>
  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>
  77         </options>
  78         <options isRequired='false'>
  79                 <name>old</name>
  80                 <description>Use old energy evaluation, treating gaps as characters</description>
  81                 <optionNames>--old</optionNames>
  82         </options>
  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>
  89         </options>
  90         <options isRequired='false'>
  91                 <name>d2</name>
  92                 <description>
  93                 Dangling energies are added for the bases adjacent to a helix on both sides
  94                 </description>
  95                 <optionNames>-d2</optionNames>
  96         </options>
  97         <options isRequired='false'>
  98                 <name>MEA Structure</name>
  99                 <description>Maximum Expected Accuracy Structure</description>
 100                 <optionNames>--MEA</optionNames>
 101         </options>
 102 <!-- Constraints are entered on the command line followed by the input .aln file
 103          Causing problems for a batch RNAalifold execution system -->
 104 <!--
 105         <option isRequired='false'>
 106                 <name>Constraints</name>
 107                 <description>Structures calculated subject to constraints</description>
 108                 <optionNames>-C</optionNames>
 109                 <validValue>
 110                         <type>String</type>
 111                 </validValue>
 112         </option> -->
 113
 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>
 123                 <validValue>
 124                         <type>Integer</type>
 125                         <min>1</min>
 126                         <max>100000</max>
 127                 </validValue>
 128         </parameters>
 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 -->
 134                 <validValue>
 135                         <type>Integer</type>
 136                         <min>1</min>
 137                         <max>100000</max>
 138                 </validValue>
 139         </parameters>
 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>
 146                 <validValue>
 147                         <type>Float</type>
 148                         <min>0</min>
 149                         <max>100</max>
 150                 </validValue>
 151         </parameters>
 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>
 157                 <validValue>
 158                         <type>Float</type>
 159                         <min>0.0000000000001</min>
 160                         <max>1.0</max>
 161                 </validValue>
 162         </parameters>
 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>
 169                 <validValue>
 170                         <type>Float</type>
 171                         <min>-274</min>
 172                         <max>1000000</max>
 173                 </validValue>
 174         </parameters>
 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>
 181                 <validValue>
 182                         <type>Integer</type>
 183                         <min>0</min>
 184                         <max>100000</max>
 185                 </validValue>
 186         </parameters>
 187         <parameters isRequired='false'>
 188                 <name>cfactor</name>
 189                 <description>weight of covariance term</description>
 190                 <optionNames>--cfactor</optionNames>
 191                 <defaultValue>1.0</defaultValue>
 192                 <validValue>
 193                         <type>Float</type>
 194                         <min>0</min>
 195                         <max>100000</max>
 196                 </validValue>
 197         </parameters>
 198         <parameters isRequired='false'>
 199                 <name>nfactor</name>
 200                 <description>penalty for non-compatible sequences in covariance term</description>
 201                 <optionNames>--nfactor</optionNames>
 202                 <defaultValue>1.0</defaultValue>
 203                 <validValue>
 204                         <type>Float</type>
 205                         <min>0</min>
 206                         <max>100000</max>
 207                 </validValue>
 208         </parameters>
 209
 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> -->
 226
 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? -->
 232
 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>
 240         </parameters>
 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>
 247                 <validValue>
 248                         <type>Float</type>
 249                         <min>0</min>
 250                         <max>100000</max>
 251                 </validValue>
 252         </parameters>
 253 </runnerConfig>