testsrc/testdata/ClustaloParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <runnerConfig>\r
   3         <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
   4         <options>\r
   5                 <name>Dealign</name>\r
   6                 <description>Dealign input sequences</description>\r
   7                 <optionNames>--dealign</optionNames>\r
   8                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
   9         </options>\r
  10         <options>\r
  11                 <name>Full distance matrix</name>\r
  12                 <description>Use full distance matrix for guide-tree calculation (slow; mBed is default)</description>\r
  13                 <optionNames>--full</optionNames>\r
  14                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
  15         </options>\r
  16         <options>\r
  17                 <name>Full distance matrix for each iteration</name>\r
  18                 <description>Use full distance matrix for guide-tree calculation during iteration (mBed is default)</description>\r
  19                 <optionNames>--full-iter</optionNames>\r
  20                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
  21         </options>\r
  22         <prmSeparator>=</prmSeparator>\r
  23         <parameters>\r
  24                 <name>Max Guide tree iterations</name>\r
  25                 <description>Maximum number of HMM iterations</description>\r
  26                 <optionNames>--max-hmm-iterations</optionNames>\r
  27                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
  28                 <defaultValue>1</defaultValue>\r
  29                 <validValue>\r
  30                         <type>Integer</type>\r
  31                         <min>1</min>\r
  32                         <max>100</max>\r
  33                 </validValue>\r
  34         </parameters>\r
  35         <parameters>\r
  36                 <name>Number of iterations (combined)</name>\r
  37                 <description>Number of (combined guide tree/HMM) iterations</description>\r
  38                 <optionNames>--iter</optionNames>\r
  39                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
  40                 <defaultValue>1</defaultValue>\r
  41                 <validValue>\r
  42                         <type>Integer</type>\r
  43                         <min>1</min>\r
  44                         <max>100</max>\r
  45                 </validValue>\r
  46         </parameters>\r
  47         <parameters>\r
  48                 <name>Max Guide tree iterations</name>\r
  49                 <description>Maximum guide tree iterations</description>\r
  50                 <optionNames>--max-guidetree-iterations</optionNames>\r
  51                 <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
  52                 <defaultValue>1</defaultValue>\r
  53                 <validValue>\r
  54                         <type>Integer</type>\r
  55                         <min>1</min>\r
  56                         <max>100</max>\r
  57                 </validValue>\r
  58         </parameters>\r
  59 </runnerConfig>\r