testsrc/testdata/RNAalifoldParameters.xml

   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'>
   6                 <name>Endgaps</name>
   7                 <description>Score pairs with endgaps same as gap-gap pairs</description>
   8                 <optionNames>-E</optionNames>
   9                 <optionNames>--endgaps</optionNames>
  10                 <defaultValue>-E</defaultValue>
  11         </options>
  12         <options isRequired='false'>
  13                 <name>Most Informative Sequence</name>
  14                 <description>Ouput Set of nucleotides with frequency > average</description>
  15                 <optionNames>--mis</optionNames>
  16         </options>
  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>
  23         </options>
  24         <options isRequired='false'>
  25                 <name>p0</name>
  26                 <description>deactivates the calculation of the pair probabilities</description>
  27                 <optionNames>-p0</optionNames>
  28         </options>
  29         <options isRequired='false'>
  30                 <name>color</name>
  31                 <description>Consensus structure plot is colored</description>
  32                 <optionNames>--color</optionNames>
  33         </options>
  34         <options isRequired='false'>
  35                 <name>Alignment</name>
  36                 <description>Output structure annotated alignment</description>
  37                 <optionNames>--aln</optionNames>
  38         </options>
  39         <options isRequired='false'>
  40                 <name>No Postscript</name>
  41                 <description>Do not produce postscript output</description>
  42                 <optionNames>--noPS</optionNames>
  43         </options>
  44         <options isRequired='false'>
  45                 <name>Circular</name>
  46                 <description>Assume circular RNA molecule</description>
  47                 <optionNames>-c</optionNames>
  48                 <optionNames>--circ</optionNames>
  49                 <defaultValue>-c</defaultValue>
  50         </options>
  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>
  58         </options>
  59         <options isRequired='false'>
  60                 <name>d2</name>
  61                 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
  62                 <optionNames>-d2</optionNames>
  63         </options>
  64         <options isRequired='false'>
  65                 <name>No LP</name>
  66                 <description>Produce Structures without lonely pairs</description>
  67                 <optionNames>--noLP</optionNames>
  68         </options>
  69         <options isRequired='false'>
  70                 <name>No GU</name>
  71                 <description>Do not allow GU pairs</description>
  72                 <optionNames>--noGU</optionNames>
  73         </options>
  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>
  78         </options>
  79         <options isRequired='false'>
  80                 <name>old</name>
  81                 <description>Use old energy evaluation, treating gaps as characters</description>
  82                 <optionNames>--old</optionNames>
  83         </options>
  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>
  90         </options>
  91         <options isRequired='false'>
  92                 <name>d2</name>
  93                 <description>
  94                 Dangling energies are added for the bases adjacent to a helix on both sides
  95                 </description>
  96                 <optionNames>-d2</optionNames>
  97         </options>
  98         <options isRequired='false'>
  99                 <name>MEA Structure</name>
 100                 <description>Maximum Expected Accuracy Structure</description>
 101                 <optionNames>--MEA</optionNames>
 102         </options>
 103 <!-- Constraints are entered on the command line followed by the input .aln file
 104          Causing problems for a batch RNAalifold execution system -->
 105 <!--
 106         <option isRequired='false'>
 107                 <name>Constraints</name>
 108                 <description>Structures calculated subject to constraints</description>
 109                 <optionNames>-C</optionNames>
 110                 <validValue>
 111                         <type>String</type>
 112                 </validValue>
 113         </option> -->
 114
 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>
 124                 <validValue>
 125                         <type>Integer</type>
 126                         <min>1</min>
 127                         <max>100000</max>
 128                 </validValue>
 129         </parameters>
 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 -->
 135                 <validValue>
 136                         <type>Integer</type>
 137                         <min>1</min>
 138                         <max>100000</max>
 139                 </validValue>
 140         </parameters>
 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>
 147                 <validValue>
 148                         <type>Float</type>
 149                         <min>0</min>
 150                         <max>100</max>
 151                 </validValue>
 152         </parameters>
 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>
 158                 <validValue>
 159                         <type>Float</type>
 160                         <min>0.0000000000001</min>
 161                         <max>1.0</max>
 162                 </validValue>
 163         </parameters>
 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>
 170                 <validValue>
 171                         <type>Float</type>
 172                         <min>-274</min>
 173                         <max>1000000</max>
 174                 </validValue>
 175         </parameters>
 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>
 182                 <validValue>
 183                         <type>Integer</type>
 184                         <min>0</min>
 185                         <max>100000</max>
 186                 </validValue>
 187         </parameters>
 188         <parameters isRequired='false'>
 189                 <name>cfactor</name>
 190                 <description>weight of covariance term</description>
 191                 <optionNames>--cfactor</optionNames>
 192                 <defaultValue>1.0</defaultValue>
 193                 <validValue>
 194                         <type>Float</type>
 195                         <min>0</min>
 196                         <max>100000</max>
 197                 </validValue>
 198         </parameters>
 199         <parameters isRequired='false'>
 200                 <name>nfactor</name>
 201                 <description>penalty for non-compatible sequences in covariance term</description>
 202                 <optionNames>--nfactor</optionNames>
 203                 <defaultValue>1.0</defaultValue>
 204                 <validValue>
 205                         <type>Float</type>
 206                         <min>0</min>
 207                         <max>100000</max>
 208                 </validValue>
 209         </parameters>
 210
 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> -->
 227
 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? -->
 233
 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>
 241         </parameters>
 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>
 248                 <validValue>
 249                         <type>Float</type>
 250                         <min>0</min>
 251                         <max>100000</max>
 252                 </validValue>
 253         </parameters>
 254 </runnerConfig>