testsrc/testdata/RNAalifoldParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
   2
   3 <runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema.dtd"
   4                         xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
   5         <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
   6         <options isRequired='false'>
   7                 <name>Endgaps</name>
   8                 <description>Score pairs with endgaps same as gap-gap pairs</description>
   9                 <optionNames>-E</optionNames>
  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         </options>
  21         <options isRequired='false'>
  22                 <name>Circular</name>
  23                 <description>Assume circular RNA molecule</description>
  24                 <optionNames>-c</optionNames>
  25         </options>
  26         <!--  Not Currently available with circular structures (-c) -->
  27         <options isRequired='false'>
  28                 <name>G-Quadruplex</name>
  29                 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
  30                 <optionNames>-g</optionNames>
  31         </options>
  32         <options isRequired='false'>
  33                 <name>d2</name>
  34                 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
  35                 <optionNames>-d2</optionNames>
  36         </options>
  37         <options isRequired='false'>
  38                 <name>No LP</name>
  39                 <description>Produce Structures without lonely pairs</description>
  40                 <optionNames>--noLP</optionNames>
  41         </options>
  42         <options isRequired='false'>
  43                 <name>No GU</name>
  44                 <description>Do not allow GU pairs</description>
  45                 <optionNames>--noGU</optionNames>
  46         </options>
  47         <options isRequired='false'>
  48                 <name>No Closing GU</name>
  49                 <description>Do not allow GU pairs at the end of sequences</description>
  50                 <optionNames>--noClosingGU</optionNames>
  51         </options>
  52         <options isRequired='false'>
  53                 <name>old</name>
  54                 <description>Use old energy evaluation, treating gaps as characters</description>
  55                 <optionNames>--old</optionNames>
  56         </options>
  57         <options isRequired='false'>
  58                 <name>Ribosum Scoring</name>
  59                 <description>Use Ribosum Scoring Matrix</description>
  60                 <optionNames>-r</optionNames>
  61         </options>
  62         <options isRequired='false'>
  63                 <name>d2</name>
  64                 <description>
  65                 Dangling energies are added for the bases adjacent to a helix on both sides
  66                 </description>
  67                 <optionNames>-d2</optionNames>
  68         </options>
  69         <options isRequired='false'>
  70                 <name>MEA Structure</name>
  71                 <description>Maximum Expected Accuracy Structure</description>
  72                 <optionNames>--MEA</optionNames>
  73         </options>
  74
  75         <prmSeparator> </prmSeparator>
  76
  77         <parameters isRequired='false'>
  78                 <name>scaling factor</name>
  79                 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
  80                 <optionNames>-S</optionNames>
  81                 <defaultValue>1.07</defaultValue>
  82                 <validValue>
  83                         <type>Float</type>
  84                         <min>0</min>
  85                         <max>100</max>
  86                 </validValue>
  87         </parameters>
  88         <parameters isRequired='false'>
  89                 <name>bppmThreshold</name>
  90                 <description>Threshold for base pair probabilities</description>
  91                 <optionNames>--bppmThreshold</optionNames>
  92                 <defaultValue>0.000001</defaultValue>
  93                 <validValue>
  94                         <type>Float</type>
  95                         <min>0.0000000000001</min>
  96                         <max>1.0</max>
  97                 </validValue>
  98         </parameters>
  99         <parameters isRequired='false'>
 100                 <name>Temperature</name>
 101                 <description>Rescale Energy parameterss to Temperature</description>
 102                 <optionNames>-T</optionNames>
 103                 <defaultValue>37</defaultValue>
 104                 <validValue>
 105                         <type>Float</type>
 106                         <min>-274</min>
 107                         <max>1000000</max>
 108                 </validValue>
 109         </parameters>
 110
 111         <parameters isRequired='false'>
 112                 <name>cfactor</name>
 113                 <description>weight of covariance term</description>
 114                 <optionNames>--cfactor</optionNames>
 115                 <defaultValue>1.0</defaultValue>
 116                 <validValue>
 117                         <type>Float</type>
 118                         <min>0</min>
 119                         <max>100000</max>
 120                 </validValue>
 121         </parameters>
 122         <parameters isRequired='false'>
 123                 <name>nfactor</name>
 124                 <description>penalty for non-compatible sequences in covariance term</description>
 125                 <optionNames>--nfactor</optionNames>
 126                 <defaultValue>1.0</defaultValue>
 127                 <validValue>
 128                         <type>Float</type>
 129                         <min>0</min>
 130                         <max>100000</max>
 131                 </validValue>
 132         </parameters>
 133
 134 </runnerConfig>