conf/settings/DisemblParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <runnerConfig>\r
   3         <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
   4         <prmSeparator>=</prmSeparator>\r
   5         <parameters>\r
   6                 <name>Savitzky-Golay smoothing frame</name>\r
   7                 <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
   8                 <optionNames>sg</optionNames>\r
   9                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  10                 <defaultValue>8</defaultValue>\r
  11                 <validValue>\r
  12                         <type>Integer</type>\r
  13                         <min>1</min>\r
  14                         <max>30</max>\r
  15                 </validValue>\r
  16         </parameters>\r
  17 <!--  \r
  18  These can be supported but not recommended to change so what's the point?\r
  19  \r
  20  Manual: Normally the default parameters should not be changed.\r
  21 \r
  22         <parameters>\r
  23                 <name>Minimum peak width</name>\r
  24                 <description>Algorithm Parameter: Minimum peak width.</description>\r
  25                 <optionNames>pw</optionNames>\r
  26                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  27                 <defaultValue>8</defaultValue>\r
  28                 <validValue>\r
  29                         <type>Integer</type>\r
  30                         <min>1</min>\r
  31                         <max>30</max>\r
  32                 </validValue>\r
  33         </parameters>\r
  34         <parameters>\r
  35                 <name>Maximum join distance</name>\r
  36                 <description>Algorithm Parameter: Maximum join distance</description>\r
  37                 <optionNames>jd</optionNames>\r
  38                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  39                 <defaultValue>4</defaultValue>\r
  40                 <validValue>\r
  41                         <type>Integer</type>\r
  42                         <min>1</min>\r
  43                         <max>30</max>\r
  44                 </validValue>\r
  45         </parameters>\r
  46         <parameters>\r
  47                 <name>Coils threshold</name>\r
  48                 <description>Stringency values for different predictor: Coils threshold</description>\r
  49                 <optionNames>ct</optionNames>\r
  50                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  51                 <defaultValue>1.2</defaultValue>\r
  52                 <validValue>\r
  53                         <type>Float</type>\r
  54                         <min>0.1</min>\r
  55                         <max>10</max>\r
  56                 </validValue>\r
  57         </parameters>\r
  58         <parameters>\r
  59                 <name>Remark465 threshold</name>\r
  60                 <description>Stringency values for different predictor: Remark465 threshold</description>\r
  61                 <optionNames>rt</optionNames>\r
  62                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  63                 <defaultValue>1.4</defaultValue>\r
  64                 <validValue>\r
  65                         <type>Float</type>\r
  66                         <min>0.1</min>\r
  67                         <max>10</max>\r
  68                 </validValue>\r
  69         </parameters>\r
  70         <parameters>\r
  71                 <name>Hot loops threshold</name>\r
  72                 <description>Stringency values for different predictor: Hot loops threshold.</description>\r
  73                 <optionNames>lt</optionNames>\r
  74                 <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
  75                 <defaultValue>1.2</defaultValue>\r
  76                 <validValue>\r
  77                         <type>Float</type>\r
  78                         <min>0.1</min>\r
  79                         <max>10</max>\r
  80                 </validValue>\r
  81         </parameters>\r
  82         -->\r
  83 \r
  84 </runnerConfig>\r