htsworkflow/pipelines/test/testdata/rta_basecalls_config.xml

   1 <?xml version="1.0" encoding="utf-8"?>\r
   2 <BaseCallAnalysis xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r
   3   <Run Name="BaseCalls">\r
   4     <BaseCallParameters>\r
   5       <ChastityThreshold>0.6</ChastityThreshold>\r
   6       <Matrix Path="">\r
   7         <AutoFlag>0</AutoFlag>\r
   8         <AutoLane>0</AutoLane>\r
   9         <Cycle>0</Cycle>\r
  10         <CycleOffset>0</CycleOffset>\r
  11         <FirstCycle>1</FirstCycle>\r
  12         <LastCycle>38</LastCycle>\r
  13         <Read>1</Read>\r
  14       </Matrix>\r
  15       <Phasing Path="">\r
  16         <AutoFlag>0</AutoFlag>\r
  17         <AutoLane>0</AutoLane>\r
  18         <Cycle>0</Cycle>\r
  19         <CycleOffset>0</CycleOffset>\r
  20         <FirstCycle>1</FirstCycle>\r
  21         <LastCycle>38</LastCycle>\r
  22         <Read>1</Read>\r
  23       </Phasing>\r
  24       <PureBases>0</PureBases>\r
  25       <SmtFilter>failed-chastity</SmtFilter>\r
  26       <SmtRelation>le</SmtRelation>\r
  27       <SmtThreshold>1.0</SmtThreshold>\r
  28     </BaseCallParameters>\r
  29     <Cycles First="1" Last="38" Number="38" />\r
  30     <Input />\r
  31     <RunParameters>\r
  32       <AutoCycleFlag>0</AutoCycleFlag>\r
  33       <BasecallFlag>0</BasecallFlag>\r
  34       <Deblocked>0</Deblocked>\r
  35       <DebugFlag>0</DebugFlag>\r
  36       <FirstRunOnlyFlag>0</FirstRunOnlyFlag>\r
  37       <ImagingReads Index="1">\r
  38         <FirstCycle>1</FirstCycle>\r
  39         <LastCycle>38</LastCycle>\r
  40         <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
  41       </ImagingReads>\r
  42       <Instrument>HWI-EAS229</Instrument>\r
  43       <IterativeMatrixFlag>0</IterativeMatrixFlag>\r
  44       <MakeFlag>0</MakeFlag>\r
  45       <MaxCycle>0</MaxCycle>\r
  46       <MinCycle>0</MinCycle>\r
  47       <Reads Index="1">\r
  48         <FirstCycle>1</FirstCycle>\r
  49         <LastCycle>38</LastCycle>\r
  50         <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
  51       </Reads>\r
  52       <RunFolder>D:\Runs\090608_HWI-EAS229_0117_4286GAAXX</RunFolder>\r
  53       <RunFolderDate>0</RunFolderDate>\r
  54       <RunFolderId>0</RunFolderId>\r
  55     </RunParameters>\r
  56     <Software Name="RTA" Version="1.4.6.0" />\r
  57     <TileSelection>\r
  58       <Lane Index="1">\r
  59         <Sample>s</Sample>\r
  60         <TileRange Max="100" Min="1" />\r
  61       </Lane>\r
  62       <Lane Index="2">\r
  63         <Sample>s</Sample>\r
  64         <TileRange Max="100" Min="1" />\r
  65       </Lane>\r
  66       <Lane Index="3">\r
  67         <Sample>s</Sample>\r
  68         <TileRange Max="100" Min="1" />\r
  69       </Lane>\r
  70       <Lane Index="4">\r
  71         <Sample>s</Sample>\r
  72         <TileRange Max="100" Min="1" />\r
  73       </Lane>\r
  74       <Lane Index="5">\r
  75         <Sample>s</Sample>\r
  76         <TileRange Max="100" Min="1" />\r
  77       </Lane>\r
  78       <Lane Index="6">\r
  79         <Sample>s</Sample>\r
  80         <TileRange Max="100" Min="1" />\r
  81       </Lane>\r
  82       <Lane Index="7">\r
  83         <Sample>s</Sample>\r
  84         <TileRange Max="100" Min="1" />\r
  85       </Lane>\r
  86       <Lane Index="8">\r
  87         <Sample>s</Sample>\r
  88         <TileRange Max="100" Min="1" />\r
  89       </Lane>\r
  90     </TileSelection>\r
  91     <Time />\r
  92     <User />\r
  93   </Run>\r
  94 </BaseCallAnalysis>