conf/settings/GLprobsParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <runnerConfig>\r
   3     <runnerClassName>compbio.runner.msa.GLprobs</runnerClassName>\r
   4 \r
   5     <options isRequired="true">\r
   6         <name>CLUSTAL format for output alignment</name>\r
   7         <description>\r
   8             CLUSTAL output format is used instead of the FASTA format\r
   9         </description>\r
  10         <optionNames>-clustalw</optionNames>\r
  11         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
  12     </options>\r
  13 \r
  14     <options isRequired="true">\r
  15         <name>Another order of sequence in output alignment</name>\r
  16         <description>\r
  17             print sequences in alignment order rather than input order\r
  18         </description>\r
  19         <optionNames>-a</optionNames>\r
  20         <optionNames>--alignment-order</optionNames>\r
  21         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
  22     </options>\r
  23 \r
  24     <prmSeparator> </prmSeparator>\r
  25 \r
  26     <parameters isRequired="false">\r
  27         <name>passes of consistency transformation</name>\r
  28         <description>\r
  29             passes of consistency transformation\r
  30         </description>\r
  31         <optionNames>-c</optionNames>\r
  32         <optionNames>--consistency</optionNames>\r
  33         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
  34         <defaultValue>2</defaultValue>\r
  35         <validValue>\r
  36             <type>Integer</type>\r
  37             <min>0</min>\r
  38             <max>5</max>\r
  39         </validValue>\r
  40      </parameters>\r
  41 \r
  42     <parameters isRequired="false">\r
  43         <name>passes of consistency transformation</name>\r
  44         <description>\r
  45             number of passes of iterative-refinement\r
  46         </description>\r
  47         <optionNames>-ir</optionNames>\r
  48         <optionNames>--iterative-refinement</optionNames>\r
  49         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
  50         <defaultValue>100</defaultValue>\r
  51         <validValue>\r
  52             <type>Integer</type>\r
  53             <min>0</min>\r
  54             <max>1000</max>\r
  55         </validValue>\r
  56      </parameters>\r
  57 \r
  58      <parameters isRequired="false">\r
  59         <name>Number of CPUs</name>\r
  60         <description>\r
  61             Number of CPU used by msaprobs. \r
  62             My default the number is equal to the total number of CPU on the system.\r
  63         </description>\r
  64         <optionNames>-num_threads</optionNames>\r
  65         <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
  66         <defaultValue>1</defaultValue>\r
  67         <validValue>\r
  68             <type>Integer</type>\r
  69             <min>1</min>\r
  70         </validValue>\r
  71     </parameters>\r
  72 \r
  73 </runnerConfig>\r