conf/settings/DisemblParameters.xml

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