conf/settings/MSAprobsParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
   2 <runnerConfig>\r
   3     <runnerClassName>compbio.runner.msa.MSAprobs</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/msaprobs.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/msaprobs.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         <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
  33         <defaultValue>2</defaultValue>\r
  34         <validValue>\r
  35             <type>Integer</type>\r
  36             <min>0</min>\r
  37             <max>5</max>\r
  38         </validValue>\r
  39      </parameters>\r
  40 \r
  41     <parameters isRequired="false">\r
  42         <name>passes of consistency transformation</name>\r
  43         <description>\r
  44                       number of passes of iterative-refinement\r
  45         </description>\r
  46         <optionNames>-ir</optionNames>\r
  47         <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
  48         <defaultValue>10</defaultValue>\r
  49         <validValue>\r
  50             <type>Integer</type>\r
  51             <min>0</min>\r
  52             <max>1000</max>\r
  53         </validValue>\r
  54      </parameters>\r
  55 \r
  56      <parameters isRequired="false">\r
  57         <name>Number of CPUs</name>\r
  58         <description>\r
  59             Number of CPU used by msaprobs. \r
  60             My default the number is equal to the total number of CPU on the system.\r
  61         </description>\r
  62         <optionNames>-num_threads</optionNames>\r
  63         <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
  64         <defaultValue>1</defaultValue>\r
  65         <validValue>\r
  66             <type>Integer</type>\r
  67             <min>1</min>\r
  68         </validValue>\r
  69     </parameters>\r
  70 </runnerConfig>\r