mev-4.0.01/config/ParameterConstraints.xml

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2 26 Feb 07 jari 1 <?xml version="1.0"?>
2 26 Feb 07 jari 2
2 26 Feb 07 jari 3 <!DOCTYPE mev_val [
2 26 Feb 07 jari 4 <!ELEMENT mev_val (script_algorithm*)>
2 26 Feb 07 jari 5
2 26 Feb 07 jari 6 <!ELEMENT script_algorithm (param_list*)>
2 26 Feb 07 jari 7 <!ATTLIST script_algorithm name CDATA #REQUIRED
2 26 Feb 07 jari 8                    input_data_dep ( true | false) #REQUIRED >
2 26 Feb 07 jari 9
2 26 Feb 07 jari 10 <!ELEMENT param_list (param+)>
2 26 Feb 07 jari 11
2 26 Feb 07 jari 12 <!ELEMENT param (constraint?)>
2 26 Feb 07 jari 13 <!ATTLIST param key CDATA #REQUIRED
2 26 Feb 07 jari 14        value_type ( boolean | int | long | float | double | string ) #REQUIRED
2 26 Feb 07 jari 15        val_level ( optional | required ) #REQUIRED >
2 26 Feb 07 jari 16
2 26 Feb 07 jari 17 <!ELEMENT constraint EMPTY>
2 26 Feb 07 jari 18 <!ATTLIST constraint min CDATA #IMPLIED
2 26 Feb 07 jari 19         max CDATA #IMPLIED>                          
2 26 Feb 07 jari 20 ]>
2 26 Feb 07 jari 21
2 26 Feb 07 jari 22 <mev_val>
2 26 Feb 07 jari 23
2 26 Feb 07 jari 24 <script_algorithm name="HCL" input_data_dep="false">
2 26 Feb 07 jari 25     
2 26 Feb 07 jari 26    <param_list>
2 26 Feb 07 jari 27
2 26 Feb 07 jari 28   <!-- algorithm specific parameters -->
2 26 Feb 07 jari 29   <param key="method-linkage" value_type="int" val_level="optional">
2 26 Feb 07 jari 30     <constraint min="0" max="2"/>
2 26 Feb 07 jari 31   </param>
2 26 Feb 07 jari 32   <param key="calculate-genes" value_type="boolean" val_level="optional"/>
2 26 Feb 07 jari 33   <param key="calculate-experiments" value_type="boolean" val_level="optional"/>
2 26 Feb 07 jari 34
2 26 Feb 07 jari 35   <!-- distance parameters -->
2 26 Feb 07 jari 36   <param key="distance-factor" value_type="float" val_level="required"/>
2 26 Feb 07 jari 37   <param key="distance-absolute" value_type="boolean" val_level="required"/>
2 26 Feb 07 jari 38   <param key="distance-function" value_type="int" val_level="required">
2 26 Feb 07 jari 39     <constraint min="0" max="9"/>
2 26 Feb 07 jari 40   </param>
2 26 Feb 07 jari 41    </param_list>
2 26 Feb 07 jari 42  </script_algorithm>
2 26 Feb 07 jari 43
2 26 Feb 07 jari 44
2 26 Feb 07 jari 45 <script_algorithm name="ST" input_data_dep="false">
2 26 Feb 07 jari 46    <param_list>
2 26 Feb 07 jari 47    <param key="exptTreeIterations" value_type="int"  val_level="optional">
2 26 Feb 07 jari 48   <constraint min="0"/>
2 26 Feb 07 jari 49    </param>
2 26 Feb 07 jari 50    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 51    <param key="drawExptTree" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 52    <param key="drawGeneTree" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 53    <param key="method-linkage" value_type="int"  val_level="required">
2 26 Feb 07 jari 54       <constraint min="0" max="2"/>
2 26 Feb 07 jari 55    </param>
2 26 Feb 07 jari 56    <param key="exptTreeAnalysisOption" value_type="int"  val_level="optional"/>
2 26 Feb 07 jari 57    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 58    <param key="geneTreeAnalysisOption" value_type="int"  val_level="optional"/>
2 26 Feb 07 jari 59    <param key="geneTreeIterations" value_type="int"  val_level="optional">
2 26 Feb 07 jari 60   <constraint min="0"/>
2 26 Feb 07 jari 61    </param>   
2 26 Feb 07 jari 62    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 63   <constraint min="0" max="9"/>
2 26 Feb 07 jari 64    </param>
2 26 Feb 07 jari 65    </param_list>
2 26 Feb 07 jari 66 </script_algorithm>
2 26 Feb 07 jari 67
2 26 Feb 07 jari 68
2 26 Feb 07 jari 69 <script_algorithm name="SOTA" input_data_dep="false">
2 26 Feb 07 jari 70    <param_list>
2 26 Feb 07 jari 71    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 72   <constraint min="0" max="9"/>
2 26 Feb 07 jari 73    </param>
2 26 Feb 07 jari 74    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 75       <constraint min="0" max="2"/>
2 26 Feb 07 jari 76    </param>
2 26 Feb 07 jari 77    <param key="end-training-diversity" value_type="float"  val_level="required">
2 26 Feb 07 jari 78   <constraint min="0"/>
2 26 Feb 07 jari 79    </param>   
2 26 Feb 07 jari 80    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 81    <param key="set-max-cluster-div" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 82    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 83    <param key="run-to-max-cycles" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 84    <param key="calc-cluster-hcl" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 85    <param key="calc-full-tree-hcl" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 86    <param key="epoch-improvement-cutoff" value_type="float"  val_level="required">
2 26 Feb 07 jari 87   <constraint min="0"/>
2 26 Feb 07 jari 88    </param>   
2 26 Feb 07 jari 89    <param key="use-cluster-variance" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 90    <param key="sota-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 91    <param key="pValue" value_type="float"  val_level="optional">
2 26 Feb 07 jari 92   <constraint min="0"/>
2 26 Feb 07 jari 93    </param>   
2 26 Feb 07 jari 94    <param key="mig_w" value_type="float"  val_level="required">
2 26 Feb 07 jari 95   <constraint min="0"/>
2 26 Feb 07 jari 96    </param>   
2 26 Feb 07 jari 97    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 98    <param key="max-epochs-per-cycle" value_type="int"  val_level="required">
2 26 Feb 07 jari 99   <constraint min="0"/>
2 26 Feb 07 jari 100    </param>   
2 26 Feb 07 jari 101    <param key="maxClusterDiv" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 102    <param key="mig_s" value_type="float"  val_level="required">
2 26 Feb 07 jari 103   <constraint min="0"/>
2 26 Feb 07 jari 104    </param>   
2 26 Feb 07 jari 105    <param key="mig_p" value_type="float"  val_level="required">
2 26 Feb 07 jari 106   <constraint min="0"/>
2 26 Feb 07 jari 107    </param>   
2 26 Feb 07 jari 108    <param key="neighborhood-level" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 109    <param key="max-number-of-cycles" value_type="int"  val_level="required">
2 26 Feb 07 jari 110   <constraint min="0"/>
2 26 Feb 07 jari 111    </param>   
2 26 Feb 07 jari 112    </param_list>
2 26 Feb 07 jari 113 </script_algorithm>
2 26 Feb 07 jari 114
2 26 Feb 07 jari 115
2 26 Feb 07 jari 116
2 26 Feb 07 jari 117 <script_algorithm name="RN" input_data_dep="false">
2 26 Feb 07 jari 118    <param_list>
2 26 Feb 07 jari 119    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 120    <param key="min-threshold" value_type="float"  val_level="required">
2 26 Feb 07 jari 121   <constraint min="0" max="1"/>
2 26 Feb 07 jari 122    </param>   
2 26 Feb 07 jari 123    <param key="threshold" value_type="float"  val_level="required">
2 26 Feb 07 jari 124   <constraint min="0" max="1"/>
2 26 Feb 07 jari 125    </param>   
2 26 Feb 07 jari 126    <param key="max-threshold" value_type="float"  val_level="required">
2 26 Feb 07 jari 127   <constraint min="0" max="1"/>
2 26 Feb 07 jari 128    </param>   
2 26 Feb 07 jari 129    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 130    <param key="rn-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 131    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 132   <constraint min="0" max="9"/>
2 26 Feb 07 jari 133    </param>
2 26 Feb 07 jari 134    <param key="filter-by-entropy" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 135    <param key="top-n-percent" value_type="float"  val_level="optional">
2 26 Feb 07 jari 136   <constraint min="0" max="100"/>
2 26 Feb 07 jari 137    </param>   
2 26 Feb 07 jari 138    <param key="use-permutation" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 139    </param_list>
2 26 Feb 07 jari 140 </script_algorithm>
2 26 Feb 07 jari 141
2 26 Feb 07 jari 142
2 26 Feb 07 jari 143   <script_algorithm name="KMC" input_data_dep="false">
2 26 Feb 07 jari 144     <param_list>
2 26 Feb 07 jari 145
2 26 Feb 07 jari 146       <!-- script info parameters 
2 26 Feb 07 jari 147       <param key="alg-type" value_type="string" val_level="required"/>
2 26 Feb 07 jari 148       <param key="output-class" value_type="string" val_level="required"/>
2 26 Feb 07 jari 149       <param key="name" value_type="string" val_level="required"/>
2 26 Feb 07 jari 150       -->
2 26 Feb 07 jari 151       <!-- algorithm specific parameters -->
2 26 Feb 07 jari 152       <param key="number-of-clusters" value_type="int" val_level="required">
2 26 Feb 07 jari 153         <constraint min="1"/>
2 26 Feb 07 jari 154       </param>
2 26 Feb 07 jari 155       <param key="number-of-iterations" value_type="int" val_level="required">
2 26 Feb 07 jari 156         <constraint min="1"/>
2 26 Feb 07 jari 157       </param>
2 26 Feb 07 jari 158       <param key="calculate-means" value_type="boolean" val_level="required"/>
2 26 Feb 07 jari 159       <param key="kmc-cluster-genes" value_type="boolean" val_level="required"/>
2 26 Feb 07 jari 160
2 26 Feb 07 jari 161       <!-- distance parameters -->
2 26 Feb 07 jari 162       <param key="distance-factor" value_type="float" val_level="required"/>
2 26 Feb 07 jari 163       <param key="distance-absolute" value_type="boolean" val_level="required"/>
2 26 Feb 07 jari 164       <param key="distance-function" value_type="int" val_level="required">
2 26 Feb 07 jari 165         <constraint min="0" max="9"/>
2 26 Feb 07 jari 166       </param>
2 26 Feb 07 jari 167
2 26 Feb 07 jari 168       <!-- HCL parameters -->
2 26 Feb 07 jari 169       <param key="hierarchical-tree" value_type="boolean" val_level="optional"/>
2 26 Feb 07 jari 170       <param key="method-linkage" value_type="int" val_level="optional">
2 26 Feb 07 jari 171         <constraint min="0" max="2"/>
2 26 Feb 07 jari 172       </param>
2 26 Feb 07 jari 173       <param key="calculate-genes" value_type="boolean" val_level="optional"/>
2 26 Feb 07 jari 174       <param key="calculate-experiments" value_type="boolean" val_level="optional"/>
2 26 Feb 07 jari 175     </param_list>
2 26 Feb 07 jari 176   </script_algorithm>
2 26 Feb 07 jari 177
2 26 Feb 07 jari 178
2 26 Feb 07 jari 179
2 26 Feb 07 jari 180 <script_algorithm name="KMS" input_data_dep="false">
2 26 Feb 07 jari 181    <param_list>
2 26 Feb 07 jari 182    <param key="calculate-means" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 183    <param key="number-of-iterations" value_type="int"  val_level="required">
2 26 Feb 07 jari 184   <constraint min="1"/>
2 26 Feb 07 jari 185    </param>   
2 26 Feb 07 jari 186    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 187    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 188    <param key="number-of-repetitions" value_type="int"  val_level="required">
2 26 Feb 07 jari 189   <constraint min="1"/>
2 26 Feb 07 jari 190    </param>   
2 26 Feb 07 jari 191    <param key="kmc-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 192    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 193    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 194    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 195       <constraint min="0" max="2"/>
2 26 Feb 07 jari 196    </param>
2 26 Feb 07 jari 197    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 198    <param key="threshold-percent" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 199    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 200   <constraint min="0" max="9"/>
2 26 Feb 07 jari 201    </param>
2 26 Feb 07 jari 202    <param key="number-of-desired-clusters" value_type="int"  val_level="required">
2 26 Feb 07 jari 203   <constraint min="1"/>
2 26 Feb 07 jari 204    </param>   
2 26 Feb 07 jari 205    </param_list>
2 26 Feb 07 jari 206 </script_algorithm>
2 26 Feb 07 jari 207
2 26 Feb 07 jari 208
2 26 Feb 07 jari 209
2 26 Feb 07 jari 210 <script_algorithm name="CAST" input_data_dep="false">
2 26 Feb 07 jari 211    <param_list>
2 26 Feb 07 jari 212    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 213    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 214    <param key="threshold" value_type="float"  val_level="required">
2 26 Feb 07 jari 215   <constraint min="0" max="1"/>
2 26 Feb 07 jari 216    </param>   
2 26 Feb 07 jari 217    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 218    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 219    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 220       <constraint min="0" max="2"/>
2 26 Feb 07 jari 221    </param>
2 26 Feb 07 jari 222    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 223    <param key="cast-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 224    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 225   <constraint min="0" max="9"/>
2 26 Feb 07 jari 226    </param>
2 26 Feb 07 jari 227    </param_list>
2 26 Feb 07 jari 228 </script_algorithm>
2 26 Feb 07 jari 229
2 26 Feb 07 jari 230
2 26 Feb 07 jari 231
2 26 Feb 07 jari 232 <script_algorithm name="QTC" input_data_dep="false">
2 26 Feb 07 jari 233    <param_list>
2 26 Feb 07 jari 234    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 235    <param key="use-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 236    <param key="min-cluster-size" value_type="int"  val_level="required">
2 26 Feb 07 jari 237   <constraint min="1"/>
2 26 Feb 07 jari 238    </param>   
2 26 Feb 07 jari 239    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 240    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 241    <param key="qtc-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 242    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 243       <constraint min="0" max="2"/>
2 26 Feb 07 jari 244    </param>
2 26 Feb 07 jari 245    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 246    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 247   <constraint min="0" max="9"/>
2 26 Feb 07 jari 248    </param>
2 26 Feb 07 jari 249    <param key="diameter" value_type="float"  val_level="required">
2 26 Feb 07 jari 250   <constraint min="0" max="1"/>
2 26 Feb 07 jari 251    </param>   
2 26 Feb 07 jari 252    </param_list>
2 26 Feb 07 jari 253 </script_algorithm>
2 26 Feb 07 jari 254
2 26 Feb 07 jari 255
2 26 Feb 07 jari 256 <script_algorithm name="GSH" input_data_dep="false">
2 26 Feb 07 jari 257    <param_list>
2 26 Feb 07 jari 258    <param key="gsh-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 259    <param key="number-of-clusters" value_type="int"  val_level="required">
2 26 Feb 07 jari 260   <constraint min="1"/>
2 26 Feb 07 jari 261    </param>   
2 26 Feb 07 jari 262    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 263    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 264    <param key="number-of-fakedMatrix" value_type="int"  val_level="required">
2 26 Feb 07 jari 265   <constraint min="1"/>
2 26 Feb 07 jari 266    </param>   
2 26 Feb 07 jari 267    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 268    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 269    <param key="number-of-swap" value_type="int"  val_level="required">
2 26 Feb 07 jari 270   <constraint min="1"/>
2 26 Feb 07 jari 271    </param>   
2 26 Feb 07 jari 272    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 273       <constraint min="0" max="2"/>
2 26 Feb 07 jari 274    </param>
2 26 Feb 07 jari 275    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 276    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 277   <constraint min="0" max="9"/>
2 26 Feb 07 jari 278    </param>
2 26 Feb 07 jari 279    </param_list>
2 26 Feb 07 jari 280 </script_algorithm>
2 26 Feb 07 jari 281
2 26 Feb 07 jari 282
2 26 Feb 07 jari 283 <script_algorithm name="SOM" input_data_dep="false">
2 26 Feb 07 jari 284    <param_list>
2 26 Feb 07 jari 285    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 286   <constraint min="0" max="9"/>
2 26 Feb 07 jari 287    </param>
2 26 Feb 07 jari 288    <param key="dimension-y" value_type="int"  val_level="required">
2 26 Feb 07 jari 289   <constraint min="1"/>
2 26 Feb 07 jari 290    </param>   
2 26 Feb 07 jari 291    <param key="dimension-x" value_type="int"  val_level="required">
2 26 Feb 07 jari 292   <constraint min="1"/>
2 26 Feb 07 jari 293    </param>   
2 26 Feb 07 jari 294    <param key="radius" value_type="float"  val_level="optional">
2 26 Feb 07 jari 295   <constraint min="0"/>
2 26 Feb 07 jari 296    </param>   
2 26 Feb 07 jari 297    <param key="is_random_vector" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 298    <param key="alpha" value_type="float"  val_level="optional">
2 26 Feb 07 jari 299   <constraint min="0"/>
2 26 Feb 07 jari 300    </param>   
2 26 Feb 07 jari 301    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 302       <constraint min="0" max="2"/>
2 26 Feb 07 jari 303    </param>
2 26 Feb 07 jari 304    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 305    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 306    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 307    <param key="iterations" value_type="int"  val_level="required">
2 26 Feb 07 jari 308   <constraint min="1"/>
2 26 Feb 07 jari 309    </param>   
2 26 Feb 07 jari 310    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 311    <param key="som-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 312    <param key="topology" value_type="string"  val_level="required"/>
2 26 Feb 07 jari 313    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 314    <param key="is_neighborhood_bubble" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 315    </param_list>
2 26 Feb 07 jari 316 </script_algorithm>
2 26 Feb 07 jari 317
2 26 Feb 07 jari 318 <script_algorithm name="FOM" input_data_dep="false">
2 26 Feb 07 jari 319    <param_list>
2 26 Feb 07 jari 320    <param key="calculate-means" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 321    <param key="method" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 322    <param key="average" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 323    <param key="cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 324    <param key="number-of-clusters" value_type="int"  val_level="optional">
2 26 Feb 07 jari 325   <constraint min="1"/>
2 26 Feb 07 jari 326    </param>   
2 26 Feb 07 jari 327    <param key="interval" value_type="float"  val_level="optional">
2 26 Feb 07 jari 328   <constraint min="0" max="1"/>
2 26 Feb 07 jari 329    </param>   
2 26 Feb 07 jari 330    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 331    <param key="iterations" value_type="int"  val_level="optional">
2 26 Feb 07 jari 332   <constraint min="1"/>
2 26 Feb 07 jari 333    </param>   
2 26 Feb 07 jari 334    <param key="fom-iterations" value_type="int"  val_level="optional">
2 26 Feb 07 jari 335   <constraint min="1"/>
2 26 Feb 07 jari 336    </param>   
2 26 Feb 07 jari 337    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 338    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 339   <constraint min="0" max="9"/>
2 26 Feb 07 jari 340    </param>   
2 26 Feb 07 jari 341    </param_list>
2 26 Feb 07 jari 342 </script_algorithm>
2 26 Feb 07 jari 343
2 26 Feb 07 jari 344
2 26 Feb 07 jari 345 <script_algorithm name="PTM" input_data_dep="true">
2 26 Feb 07 jari 346    <param_list>
2 26 Feb 07 jari 347    <param key="hierarchical-tree" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 348    <param key="use-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 349    <param key="threshold" value_type="float"  val_level="required">
2 26 Feb 07 jari 350   <constraint min="0" max="1"/>
2 26 Feb 07 jari 351    </param>   
2 26 Feb 07 jari 352    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 353    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 354    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 355       <constraint min="0" max="2"/>
2 26 Feb 07 jari 356    </param>
2 26 Feb 07 jari 357    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 358    <param key="useR" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 359    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 360   <constraint min="0" max="9"/>
2 26 Feb 07 jari 361    </param>
2 26 Feb 07 jari 362    <param key="ptm-cluster-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 363    </param_list>
2 26 Feb 07 jari 364 </script_algorithm>
2 26 Feb 07 jari 365
2 26 Feb 07 jari 366
2 26 Feb 07 jari 367 <script_algorithm name="TTEST" input_data_dep="true">
2 26 Feb 07 jari 368    <param_list>
2 26 Feb 07 jari 369    <param key="distance-function" value_type="int"  val_level="optional">
2 26 Feb 07 jari 370   <constraint min="0" max="9"/>
2 26 Feb 07 jari 371    </param>
2 26 Feb 07 jari 372    <param key="alpha" value_type="float"  val_level="optional">
2 26 Feb 07 jari 373   <constraint min="0" max="1"/>
2 26 Feb 07 jari 374    </param>   
2 26 Feb 07 jari 375    <param key="useWelchDf" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 376    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 377       <constraint min="0" max="2"/>
2 26 Feb 07 jari 378    </param>
2 26 Feb 07 jari 379    <param key="significance-method" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 380    <param key="num-combs" value_type="int"  val_level="required">
2 26 Feb 07 jari 381   <constraint min="1"/>
2 26 Feb 07 jari 382    </param>   
2 26 Feb 07 jari 383    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 384    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 385    <param key="use-all-combs" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 386    <param key="distance-absolute" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 387    <param key="is-permut" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 388    <param key="distance-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 389    <param key="oneClassMean" value_type="double"  val_level="optional">
2 26 Feb 07 jari 390   <constraint min="0.0"/>
2 26 Feb 07 jari 391    </param>   
2 26 Feb 07 jari 392    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 393    <param key="tTestDesign" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 394    </param_list>
2 26 Feb 07 jari 395 </script_algorithm>
2 26 Feb 07 jari 396
2 26 Feb 07 jari 397
2 26 Feb 07 jari 398
2 26 Feb 07 jari 399 <script_algorithm name="SAM" input_data_dep="true">
2 26 Feb 07 jari 400    <param_list>
2 26 Feb 07 jari 401    <param key="distance-function" value_type="int"  val_level="optional">
2 26 Feb 07 jari 402   <constraint min="0" max="9"/>
2 26 Feb 07 jari 403    </param>
2 26 Feb 07 jari 404    <param key="useAllUniquePerms" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 405    <param key="saveImputedMatrix" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 406    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 407       <constraint min="0" max="2"/>
2 26 Feb 07 jari 408    </param>
2 26 Feb 07 jari 409    <param key="num-combs" value_type="int"  val_level="optional">
2 26 Feb 07 jari 410   <constraint min="1"/>
2 26 Feb 07 jari 411    </param>   
2 26 Feb 07 jari 412    <param key="userPercentile" value_type="double"  val_level="optional"/>
2 26 Feb 07 jari 413    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 414    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 415    <param key="permit-graph-interaction" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 416    <param key="useTusherEtAlS0" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 417    <param key="num-neighbors" value_type="int"  val_level="optional">
2 26 Feb 07 jari 418   <constraint min="1"/>
2 26 Feb 07 jari 419    </param>   
2 26 Feb 07 jari 420    <param key="distance-absolute" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 421    <param key="use-previous-graph" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 422    <param key="distance-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 423    <param key="calculateQLowestFDR" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 424    <param key="study-design" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 425    <param key="delta" value_type="double"  val_level="required">
2 26 Feb 07 jari 426   <constraint min="0"/>
2 26 Feb 07 jari 427    </param>
2 26 Feb 07 jari 428    <param key="oneClassMean" type="float" val_level="optional"/>   
2 26 Feb 07 jari 429    <param key="use-k-nearest" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 430    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 431    </param_list>
2 26 Feb 07 jari 432 </script_algorithm>
2 26 Feb 07 jari 433
2 26 Feb 07 jari 434
2 26 Feb 07 jari 435
2 26 Feb 07 jari 436 <script_algorithm name="ANOVA" input_data_dep="true">
2 26 Feb 07 jari 437    <param_list>
2 26 Feb 07 jari 438    <param key="numGroups" value_type="int"  val_level="required">
2 26 Feb 07 jari 439   <constraint min="2"/>
2 26 Feb 07 jari 440    </param>   
2 26 Feb 07 jari 441    <param key="distance-absolute" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 442    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 443    <param key="correction-method" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 444    <param key="alpha" value_type="double"  val_level="required">
2 26 Feb 07 jari 445   <constraint min="0" max="1"/>
2 26 Feb 07 jari 446    </param>   
2 26 Feb 07 jari 447    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 448    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 449    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 450       <constraint min="0" max="2"/>
2 26 Feb 07 jari 451    </param>
2 26 Feb 07 jari 452    <param key="distance-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 453    <param key="distance-function" value_type="int"  val_level="optional">
2 26 Feb 07 jari 454   <constraint min="0" max="9"/>
2 26 Feb 07 jari 455    </param>
2 26 Feb 07 jari 456    </param_list>
2 26 Feb 07 jari 457 </script_algorithm>
2 26 Feb 07 jari 458
2 26 Feb 07 jari 459
2 26 Feb 07 jari 460
2 26 Feb 07 jari 461 <script_algorithm name="TFA" input_data_dep="true">
2 26 Feb 07 jari 462    <param_list>
2 26 Feb 07 jari 463    <param key="hierarchical-tree" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 464    <param key="distance-absolute" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 465    <param key="alpha" value_type="float"  val_level="required">
2 26 Feb 07 jari 466   <constraint min="0" max="1"/>
2 26 Feb 07 jari 467    </param>   
2 26 Feb 07 jari 468    <param key="isBalancedDesign" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 469    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 470    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 471    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 472       <constraint min="0" max="2"/>
2 26 Feb 07 jari 473    </param>
2 26 Feb 07 jari 474    <param key="distance-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 475    <param key="numPerms" value_type="int"  val_level="optional">
2 26 Feb 07 jari 476   <constraint min="1"/>
2 26 Feb 07 jari 477    </param>   
2 26 Feb 07 jari 478    <param key="distance-function" value_type="int"  val_level="optional">
2 26 Feb 07 jari 479   <constraint min="0" max="9"/>
2 26 Feb 07 jari 480    </param>
2 26 Feb 07 jari 481    <param key="allCellsHaveOneSample" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 482    <param key="usePerms" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 483    <param key="adjustmentMethod" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 484    </param_list>
2 26 Feb 07 jari 485 </script_algorithm>
2 26 Feb 07 jari 486
2 26 Feb 07 jari 487
2 26 Feb 07 jari 488 <script_algorithm name="SVM" input_data_dep="true">
2 26 Feb 07 jari 489    <param_list>
2 26 Feb 07 jari 490    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 491   <constraint min="0" max="9"/>
2 26 Feb 07 jari 492    </param>
2 26 Feb 07 jari 493    <param key="constant" value_type="float"  val_level="optional">
2 26 Feb 07 jari 494   <constraint min="0"/>
2 26 Feb 07 jari 495    </param>   
2 26 Feb 07 jari 496    <param key="constrain-weights" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 497    <param key="linkage-method" value_type="int"  val_level="optional">
2 26 Feb 07 jari 498       <constraint min="0" max="2"/>
2 26 Feb 07 jari 499    </param>
2 26 Feb 07 jari 500    <param key="negative-diagonal" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 501    <param key="seed" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 502    <param key="used-classification-editor" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 503    <param key="coefficient" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 504    <param key="width-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 505    <param key="power" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 506    <param key="negative-constraint" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 507    <param key="calculate-samples-hcl" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 508    <param key="is-classify" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 509    <param key="mode" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 510    <param key="diagonal-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 511    <param key="radial" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 512    <param key="calculate-hcl" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 513    <param key="convergence-threshold" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 514    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 515    <param key="normalize" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 516    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 517    <param key="positive-constraint" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 518    <param key="positive-diagonal" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 519    <param key="classify-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 520    <param key="calculate-genes-hcl" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 521    </param_list>
2 26 Feb 07 jari 522 </script_algorithm>
2 26 Feb 07 jari 523
2 26 Feb 07 jari 524
2 26 Feb 07 jari 525
2 26 Feb 07 jari 526
2 26 Feb 07 jari 527 <script_algorithm name="KNNC" input_data_dep="true">
2 26 Feb 07 jari 528    <param_list>
2 26 Feb 07 jari 529    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 530   <constraint min="0" max="9"/>
2 26 Feb 07 jari 531    </param>
2 26 Feb 07 jari 532    <param key="numClasses" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 533    <param key="method-linkage" value_type="int"  val_level="optional">
2 26 Feb 07 jari 534       <constraint min="0" max="2"/>
2 26 Feb 07 jari 535    </param>
2 26 Feb 07 jari 536    <param key="numVarFilteredVectors" value_type="int"  val_level="optional"/>
2 26 Feb 07 jari 537    <param key="useVarianceFilter" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 538    <param key="calculate-genes" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 539    <param key="calculate-experiments" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 540    <param key="classifyGenes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 541    <param key="validate" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 542    <param key="numNeighbors" value_type="int"  val_level="required">
2 26 Feb 07 jari 543   <constraint min="1"/>
2 26 Feb 07 jari 544    </param>   
2 26 Feb 07 jari 545    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 546    <param key="distance-factor" value_type="float"  val_level="optional"/>
2 26 Feb 07 jari 547    <param key="useCorrelFilter" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 548    <param key="numPerms" value_type="int"  val_level="optional">
2 26 Feb 07 jari 549   <constraint min="1"/>
2 26 Feb 07 jari 550    </param>   
2 26 Feb 07 jari 551    <param key="correlPValue" value_type="boolean"  val_level="optional">
2 26 Feb 07 jari 552   <constraint min="0" max="1"/>
2 26 Feb 07 jari 553    </param>   
2 26 Feb 07 jari 554    <param key="hierarchical-tree" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 555    </param_list>
2 26 Feb 07 jari 556 </script_algorithm>
2 26 Feb 07 jari 557
2 26 Feb 07 jari 558
2 26 Feb 07 jari 559
2 26 Feb 07 jari 560 <script_algorithm name="GDM" input_data_dep="false">
2 26 Feb 07 jari 561    <param_list>
2 26 Feb 07 jari 562    <param key="display-interval" value_type="int"  val_level="required">
2 26 Feb 07 jari 563   <constraint min="1"/>
2 26 Feb 07 jari 564    </param>   
2 26 Feb 07 jari 565    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 566    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 567    <param key="gdm-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 568    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 569   <constraint min="0" max="9"/>
2 26 Feb 07 jari 570    </param>   
2 26 Feb 07 jari 571    </param_list>
2 26 Feb 07 jari 572 </script_algorithm>
2 26 Feb 07 jari 573
2 26 Feb 07 jari 574
2 26 Feb 07 jari 575 <script_algorithm name="COA" input_data_dep="false">
2 26 Feb 07 jari 576    <param_list>
2 26 Feb 07 jari 577    <param key="numNeighbors" value_type="int"  val_level="required">
2 26 Feb 07 jari 578   <constraint min="1"/>
2 26 Feb 07 jari 579    </param>   
2 26 Feb 07 jari 580    </param_list>
2 26 Feb 07 jari 581 </script_algorithm>
2 26 Feb 07 jari 582
2 26 Feb 07 jari 583
2 26 Feb 07 jari 584 <script_algorithm name="PCA" input_data_dep="false">
2 26 Feb 07 jari 585    <param_list>
2 26 Feb 07 jari 586    <param key="pca-mode" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 587    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 588    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 589    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 590   <constraint min="0" max="9"/>
2 26 Feb 07 jari 591    </param>   
2 26 Feb 07 jari 592    </param_list>
2 26 Feb 07 jari 593 </script_algorithm>
2 26 Feb 07 jari 594
2 26 Feb 07 jari 595
2 26 Feb 07 jari 596 <script_algorithm name="Terrain" input_data_dep="false">
2 26 Feb 07 jari 597    <param_list>
2 26 Feb 07 jari 598    <param key="use-genes" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 599    <param key="neighbors" value_type="int"  val_level="required"/>
2 26 Feb 07 jari 600    <param key="distance-factor" value_type="float"  val_level="required"/>
2 26 Feb 07 jari 601    <param key="distance-absolute" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 602    <param key="distance-function" value_type="int"  val_level="required">
2 26 Feb 07 jari 603   <constraint min="0" max="9"/>
2 26 Feb 07 jari 604    </param>   
2 26 Feb 07 jari 605    </param_list>
2 26 Feb 07 jari 606 </script_algorithm>
2 26 Feb 07 jari 607
2 26 Feb 07 jari 608
2 26 Feb 07 jari 609 <script_algorithm name="EASE" input_data_dep="true">
2 26 Feb 07 jari 610    <param_list>
2 26 Feb 07 jari 611    <param key="population-file-name" value_type="string"  val_level="optional"/>
2 26 Feb 07 jari 612    <param key="trim-option" value_type="string"  val_level="required"/>
2 26 Feb 07 jari 613    <param key="run-permutation-analysis" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 614    <param key="bonferroni-step-down-correction" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 615    <param key="report-ease-score" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 616    <param key="annotation-key-type" value_type="string"  val_level="required"/>
2 26 Feb 07 jari 617    <param key="perform-cluster-analysis" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 618    <param key="bonferroni-correction" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 619    <param key="p-value-corrections" value_type="boolean"  val_level="required"/>
2 26 Feb 07 jari 620    <param key="trim-value" value_type="string"  val_level="optional"/>
2 26 Feb 07 jari 621    <param key="permutation-count" value_type="int"  val_level="optional"/>
2 26 Feb 07 jari 622    <param key="sidak-correction" value_type="boolean"  val_level="optional"/>
2 26 Feb 07 jari 623    <param key="converter-file-name" value_type="string"  val_level="optional"/>
2 26 Feb 07 jari 624    </param_list>
2 26 Feb 07 jari 625 </script_algorithm>
2 26 Feb 07 jari 626
2 26 Feb 07 jari 627 </mev_val>
2 26 Feb 07 jari 628
2 26 Feb 07 jari 629
2 26 Feb 07 jari 630

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