conf/settings/DisemblParameters.xml

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