htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.10.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>1</AutoFlag>\r
   8         <AutoLane>8</AutoLane>\r
   9         <Cycle>1</Cycle>\r
  10         <CycleOffset>0</CycleOffset>\r
  11         <FirstCycle>1</FirstCycle>\r
  12         <LastCycle>100</LastCycle>\r
  13         <Read>1</Read>\r
  14       </Matrix>\r
  15       <Matrix Path="">\r
  16         <AutoFlag>1</AutoFlag>\r
  17         <AutoLane>8</AutoLane>\r
  18         <Cycle>101</Cycle>\r
  19         <CycleOffset>0</CycleOffset>\r
  20         <FirstCycle>101</FirstCycle>\r
  21         <LastCycle>200</LastCycle>\r
  22         <Read>2</Read>\r
  23       </Matrix>\r
  24       <Phasing Path="">\r
  25         <AutoFlag>1</AutoFlag>\r
  26         <AutoLane>8</AutoLane>\r
  27         <Cycle>2</Cycle>\r
  28         <CycleOffset>1</CycleOffset>\r
  29         <FirstCycle>1</FirstCycle>\r
  30         <LastCycle>100</LastCycle>\r
  31         <Read>1</Read>\r
  32         <PhasingRate>0</PhasingRate>\r
  33         <PrephasingRate>0</PrephasingRate>\r
  34       </Phasing>\r
  35       <Phasing Path="">\r
  36         <AutoFlag>1</AutoFlag>\r
  37         <AutoLane>8</AutoLane>\r
  38         <Cycle>102</Cycle>\r
  39         <CycleOffset>1</CycleOffset>\r
  40         <FirstCycle>101</FirstCycle>\r
  41         <LastCycle>200</LastCycle>\r
  42         <Read>2</Read>\r
  43         <PhasingRate>0</PhasingRate>\r
  44         <PrephasingRate>0</PrephasingRate>\r
  45       </Phasing>\r
  46       <PureBases>0</PureBases>\r
  47       <SmtFilter>failed-chastity</SmtFilter>\r
  48       <SmtRelation>le</SmtRelation>\r
  49       <SmtThreshold>1.0</SmtThreshold>\r
  50     </BaseCallParameters>\r
  51     <Cycles First="1" Last="200" Number="200" />\r
  52     <Input />\r
  53     <RunParameters>\r
  54       <AutoCycleFlag>0</AutoCycleFlag>\r
  55       <BasecallFlag>0</BasecallFlag>\r
  56       <Deblocked>0</Deblocked>\r
  57       <DebugFlag>0</DebugFlag>\r
  58       <FirstRunOnlyFlag>0</FirstRunOnlyFlag>\r
  59       <ImagingReads Index="1">\r
  60         <FirstCycle>1</FirstCycle>\r
  61         <LastCycle>100</LastCycle>\r
  62       </ImagingReads>\r
  63       <ImagingReads Index="2">\r
  64         <FirstCycle>101</FirstCycle>\r
  65         <LastCycle>200</LastCycle>\r
  66         <RunFolder>110420_SN787_0069_AA01CCABAXX</RunFolder>\r
  67       </ImagingReads>\r
  68       <Instrument>HWI-ST0787</Instrument>\r
  69       <IterativeMatrixFlag>0</IterativeMatrixFlag>\r
  70       <MakeFlag>0</MakeFlag>\r
  71       <MaxCycle>0</MaxCycle>\r
  72       <MinCycle>0</MinCycle>\r
  73       <Reads Index="1">\r
  74         <FirstCycle>1</FirstCycle>\r
  75         <LastCycle>100</LastCycle>\r
  76       </Reads>\r
  77       <Reads Index="2">\r
  78         <FirstCycle>101</FirstCycle>\r
  79         <LastCycle>200</LastCycle>\r
  80         <RunFolder>110420_SN787_0069_AA01CCABAXX</RunFolder>\r
  81       </Reads>\r
  82       <RunFolder>110420_SN787_0069_AA01CCABAXX</RunFolder>\r
  83       <RunFolderDate>110420</RunFolderDate>\r
  84       <RunFolderId>0069</RunFolderId>\r
  85       <QTableVersion>PL14</QTableVersion>\r
  86     </RunParameters>\r
  87     <Software Name="RTA" Version="1.10.36.0" />\r
  88     <TileSelection>\r
  89       <Lane Index="1">\r
  90         <Sample>s</Sample>\r
  91         <Tile>1104</Tile>\r
  92         <Tile>1102</Tile>\r
  93         <Tile>1103</Tile>\r
  94         <Tile>1101</Tile>\r
  95         <Tile>1105</Tile>\r
  96         <Tile>1106</Tile>\r
  97         <Tile>1107</Tile>\r
  98         <Tile>1108</Tile>\r
  99         <Tile>1201</Tile>\r
 100         <Tile>1202</Tile>\r
 101         <Tile>1203</Tile>\r
 102         <Tile>1204</Tile>\r
 103         <Tile>1205</Tile>\r
 104         <Tile>1206</Tile>\r
 105         <Tile>1207</Tile>\r
 106         <Tile>1208</Tile>\r
 107         <Tile>2101</Tile>\r
 108         <Tile>2102</Tile>\r
 109         <Tile>2103</Tile>\r
 110         <Tile>2104</Tile>\r
 111         <Tile>2105</Tile>\r
 112         <Tile>2106</Tile>\r
 113         <Tile>2107</Tile>\r
 114         <Tile>2108</Tile>\r
 115         <Tile>2201</Tile>\r
 116         <Tile>2202</Tile>\r
 117         <Tile>2203</Tile>\r
 118         <Tile>2204</Tile>\r
 119         <Tile>2205</Tile>\r
 120         <Tile>2206</Tile>\r
 121         <Tile>2207</Tile>\r
 122         <Tile>2208</Tile>\r
 123       </Lane>\r
 124       <Lane Index="2">\r
 125         <Sample>s</Sample>\r
 126         <Tile>1101</Tile>\r
 127         <Tile>1102</Tile>\r
 128         <Tile>1103</Tile>\r
 129         <Tile>1104</Tile>\r
 130         <Tile>1105</Tile>\r
 131         <Tile>1106</Tile>\r
 132         <Tile>1107</Tile>\r
 133         <Tile>1108</Tile>\r
 134         <Tile>1201</Tile>\r
 135         <Tile>1202</Tile>\r
 136         <Tile>1203</Tile>\r
 137         <Tile>1204</Tile>\r
 138         <Tile>1205</Tile>\r
 139         <Tile>1206</Tile>\r
 140         <Tile>1207</Tile>\r
 141         <Tile>1208</Tile>\r
 142         <Tile>2101</Tile>\r
 143         <Tile>2102</Tile>\r
 144         <Tile>2103</Tile>\r
 145         <Tile>2104</Tile>\r
 146         <Tile>2105</Tile>\r
 147         <Tile>2106</Tile>\r
 148         <Tile>2107</Tile>\r
 149         <Tile>2108</Tile>\r
 150         <Tile>2201</Tile>\r
 151         <Tile>2202</Tile>\r
 152         <Tile>2203</Tile>\r
 153         <Tile>2204</Tile>\r
 154         <Tile>2205</Tile>\r
 155         <Tile>2206</Tile>\r
 156         <Tile>2207</Tile>\r
 157         <Tile>2208</Tile>\r
 158       </Lane>\r
 159       <Lane Index="3">\r
 160         <Sample>s</Sample>\r
 161         <Tile>1101</Tile>\r
 162         <Tile>1102</Tile>\r
 163         <Tile>1103</Tile>\r
 164         <Tile>1104</Tile>\r
 165         <Tile>1105</Tile>\r
 166         <Tile>1106</Tile>\r
 167         <Tile>1107</Tile>\r
 168         <Tile>1108</Tile>\r
 169         <Tile>1201</Tile>\r
 170         <Tile>1202</Tile>\r
 171         <Tile>1203</Tile>\r
 172         <Tile>1204</Tile>\r
 173         <Tile>1205</Tile>\r
 174         <Tile>1206</Tile>\r
 175         <Tile>1207</Tile>\r
 176         <Tile>1208</Tile>\r
 177         <Tile>2101</Tile>\r
 178         <Tile>2102</Tile>\r
 179         <Tile>2103</Tile>\r
 180         <Tile>2104</Tile>\r
 181         <Tile>2105</Tile>\r
 182         <Tile>2106</Tile>\r
 183         <Tile>2107</Tile>\r
 184         <Tile>2108</Tile>\r
 185         <Tile>2201</Tile>\r
 186         <Tile>2202</Tile>\r
 187         <Tile>2203</Tile>\r
 188         <Tile>2204</Tile>\r
 189         <Tile>2206</Tile>\r
 190         <Tile>2205</Tile>\r
 191         <Tile>2208</Tile>\r
 192         <Tile>2207</Tile>\r
 193       </Lane>\r
 194       <Lane Index="4">\r
 195         <Sample>s</Sample>\r
 196         <Tile>1102</Tile>\r
 197         <Tile>1101</Tile>\r
 198         <Tile>1104</Tile>\r
 199         <Tile>1106</Tile>\r
 200         <Tile>1103</Tile>\r
 201         <Tile>1105</Tile>\r
 202         <Tile>1108</Tile>\r
 203         <Tile>1107</Tile>\r
 204         <Tile>1201</Tile>\r
 205         <Tile>1202</Tile>\r
 206         <Tile>1205</Tile>\r
 207         <Tile>1204</Tile>\r
 208         <Tile>1203</Tile>\r
 209         <Tile>1206</Tile>\r
 210         <Tile>2101</Tile>\r
 211         <Tile>1208</Tile>\r
 212         <Tile>1207</Tile>\r
 213         <Tile>2102</Tile>\r
 214         <Tile>2105</Tile>\r
 215         <Tile>2106</Tile>\r
 216         <Tile>2103</Tile>\r
 217         <Tile>2104</Tile>\r
 218         <Tile>2201</Tile>\r
 219         <Tile>2202</Tile>\r
 220         <Tile>2107</Tile>\r
 221         <Tile>2108</Tile>\r
 222         <Tile>2205</Tile>\r
 223         <Tile>2206</Tile>\r
 224         <Tile>2203</Tile>\r
 225         <Tile>2204</Tile>\r
 226         <Tile>2208</Tile>\r
 227         <Tile>2207</Tile>\r
 228       </Lane>\r
 229       <Lane Index="5">\r
 230         <Sample>s</Sample>\r
 231         <Tile>1101</Tile>\r
 232         <Tile>1102</Tile>\r
 233         <Tile>1105</Tile>\r
 234         <Tile>1106</Tile>\r
 235         <Tile>1103</Tile>\r
 236         <Tile>1104</Tile>\r
 237         <Tile>1201</Tile>\r
 238         <Tile>1202</Tile>\r
 239         <Tile>1107</Tile>\r
 240         <Tile>1108</Tile>\r
 241         <Tile>1205</Tile>\r
 242         <Tile>1206</Tile>\r
 243         <Tile>1203</Tile>\r
 244         <Tile>2101</Tile>\r
 245         <Tile>1204</Tile>\r
 246         <Tile>2102</Tile>\r
 247         <Tile>1207</Tile>\r
 248         <Tile>2105</Tile>\r
 249         <Tile>2106</Tile>\r
 250         <Tile>1208</Tile>\r
 251         <Tile>2103</Tile>\r
 252         <Tile>2201</Tile>\r
 253         <Tile>2202</Tile>\r
 254         <Tile>2104</Tile>\r
 255         <Tile>2205</Tile>\r
 256         <Tile>2107</Tile>\r
 257         <Tile>2206</Tile>\r
 258         <Tile>2108</Tile>\r
 259         <Tile>2203</Tile>\r
 260         <Tile>2204</Tile>\r
 261         <Tile>2207</Tile>\r
 262         <Tile>2208</Tile>\r
 263       </Lane>\r
 264       <Lane Index="6">\r
 265         <Sample>s</Sample>\r
 266         <Tile>1101</Tile>\r
 267         <Tile>1102</Tile>\r
 268         <Tile>1105</Tile>\r
 269         <Tile>1106</Tile>\r
 270         <Tile>1201</Tile>\r
 271         <Tile>1103</Tile>\r
 272         <Tile>1202</Tile>\r
 273         <Tile>1104</Tile>\r
 274         <Tile>1205</Tile>\r
 275         <Tile>1107</Tile>\r
 276         <Tile>1206</Tile>\r
 277         <Tile>1108</Tile>\r
 278         <Tile>2101</Tile>\r
 279         <Tile>1203</Tile>\r
 280         <Tile>2102</Tile>\r
 281         <Tile>1204</Tile>\r
 282         <Tile>2105</Tile>\r
 283         <Tile>2106</Tile>\r
 284         <Tile>1207</Tile>\r
 285         <Tile>1208</Tile>\r
 286         <Tile>2201</Tile>\r
 287         <Tile>2202</Tile>\r
 288         <Tile>2103</Tile>\r
 289         <Tile>2104</Tile>\r
 290         <Tile>2205</Tile>\r
 291         <Tile>2206</Tile>\r
 292         <Tile>2107</Tile>\r
 293         <Tile>2108</Tile>\r
 294         <Tile>2203</Tile>\r
 295         <Tile>2204</Tile>\r
 296         <Tile>2207</Tile>\r
 297         <Tile>2208</Tile>\r
 298       </Lane>\r
 299       <Lane Index="7">\r
 300         <Sample>s</Sample>\r
 301         <Tile>1101</Tile>\r
 302         <Tile>1102</Tile>\r
 303         <Tile>1105</Tile>\r
 304         <Tile>1106</Tile>\r
 305         <Tile>1201</Tile>\r
 306         <Tile>1202</Tile>\r
 307         <Tile>1205</Tile>\r
 308         <Tile>1103</Tile>\r
 309         <Tile>1104</Tile>\r
 310         <Tile>1206</Tile>\r
 311         <Tile>2101</Tile>\r
 312         <Tile>1107</Tile>\r
 313         <Tile>1108</Tile>\r
 314         <Tile>2102</Tile>\r
 315         <Tile>2105</Tile>\r
 316         <Tile>1203</Tile>\r
 317         <Tile>1204</Tile>\r
 318         <Tile>2106</Tile>\r
 319         <Tile>2201</Tile>\r
 320         <Tile>1207</Tile>\r
 321         <Tile>1208</Tile>\r
 322         <Tile>2205</Tile>\r
 323         <Tile>2202</Tile>\r
 324         <Tile>2103</Tile>\r
 325         <Tile>2104</Tile>\r
 326         <Tile>2206</Tile>\r
 327         <Tile>2107</Tile>\r
 328         <Tile>2108</Tile>\r
 329         <Tile>2203</Tile>\r
 330         <Tile>2204</Tile>\r
 331         <Tile>2207</Tile>\r
 332         <Tile>2208</Tile>\r
 333       </Lane>\r
 334       <Lane Index="8">\r
 335         <Sample>s</Sample>\r
 336         <Tile>1101</Tile>\r
 337         <Tile>1105</Tile>\r
 338         <Tile>1102</Tile>\r
 339         <Tile>1106</Tile>\r
 340         <Tile>1201</Tile>\r
 341         <Tile>1205</Tile>\r
 342         <Tile>1202</Tile>\r
 343         <Tile>1103</Tile>\r
 344         <Tile>2101</Tile>\r
 345         <Tile>1206</Tile>\r
 346         <Tile>1104</Tile>\r
 347         <Tile>1107</Tile>\r
 348         <Tile>2105</Tile>\r
 349         <Tile>2102</Tile>\r
 350         <Tile>1108</Tile>\r
 351         <Tile>1203</Tile>\r
 352         <Tile>2201</Tile>\r
 353         <Tile>2106</Tile>\r
 354         <Tile>1204</Tile>\r
 355         <Tile>1207</Tile>\r
 356         <Tile>2205</Tile>\r
 357         <Tile>2202</Tile>\r
 358         <Tile>1208</Tile>\r
 359         <Tile>2103</Tile>\r
 360         <Tile>2206</Tile>\r
 361         <Tile>2104</Tile>\r
 362         <Tile>2107</Tile>\r
 363         <Tile>2108</Tile>\r
 364         <Tile>2203</Tile>\r
 365         <Tile>2204</Tile>\r
 366         <Tile>2207</Tile>\r
 367         <Tile>2208</Tile>\r
 368       </Lane>\r
 369     </TileSelection>\r
 370     <Time />\r
 371     <User />\r
 372   </Run>\r
 373 </BaseCallAnalysis>