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date Thu, 21 Jan 2016 00:34:58 -0500
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1 <tool id="cddssddspqapsssp2" name="Create script from the template file ">
2 <description>
3 used to create script file from user given input to build a model
4 </description>
5 <requirements>
6 <requirement type="set_environment">R_ROOT_DIR</requirement>
7 <requirement type="package" version="3.2.0">R</requirement>
8 <requirement type="package" version="1.0.0">caret-tools</requirement>
9 </requirements>
10 <command interpreter="python">
11 #if $OPTION11.PARAMETERS == "Advance"
12 tool2/modelBuilding.py --method $METHOD $RDATA --getdatainfoeval $OPTION11.GETDATAINFOEVAL --getdatainfoecho $OPTION11.GETDATAINFOECHO --getdatainforesult $OPTION11.GETDATAINFORESULT --missingfiltereval $OPTION11.CON1.MISSINGFILTEREVAL --missingfilterecho $OPTION11.CON1.MISSINGFILTERECHO --missingfilterresult $OPTION11.CON1.MISSINGFILTERRESULT --missingfilterthreshc $OPTION11.CON1.MISSINGFILTERTHRESHC --missingfilterthreshr $OPTION11.CON1.MISSINGFILTERTHRESHR --pcaeval $OPTION11.PCAEVAL --pcaecho $OPTION11.PCAECHO --pcaresult $OPTION11.PCARESULT --pcacomp $OPTION11.PCACOMP --pcaploteval $OPTION11.PCAPLOTEVAL --pcaplotecho $OPTION11.PCAPLOTECHO --pcaplotresult $OPTION11.PCAPLOTRESULT --pcaplotfig $OPTION11.PCAPLOTFIG --initialdataspliteval $OPTION11.CON2.INITIALDATASPLITEVAL --initialdatasplitecho $OPTION11.CON2.INITIALDATASPLITECHO --initialdatasplitresult $OPTION11.CON2.INITIALDATASPLITRESULT --saampling $OPTION11.CON2.SAAMPLING --percent $OPTION11.CON2.PERCENT --nzveval $OPTION11.CON3.NZVEVAL --nzvresult $OPTION11.CON3.NZVRESULT --nzvecho $OPTION11.CON3.NZVECHO --corrfiltereval $OPTION11.CON4.CORRFILTEREVAL --corrfilterresult $OPTION11.CON4.CORRFILTERRESULT --corrfilterecho $OPTION11.CON4.CORRFILTERECHO --threshholdcor $OPTION11.CON4.THRESHHOLDCOR --preproceval $OPTION11.CON5.PREPROCEVAL --preprocecho $OPTION11.CON5.PREPROCECHO --preprocresult $OPTION11.CON5.PREPROCRESULT --setupworkersecho $OPTION11.SETUPWORKERSECHO --setupworkersresult $OPTION11.SETUPWORKERSRESULT --numworkers $OPTION11.NUMWORKERS --setupresamplingecho $OPTION11.CON6.SETUPRESAMPLINGECHO --setupresamplingresult $OPTION11.CON6.SETUPRESAMPLINGRESULT --resampname $OPTION11.CON6.RESAMPNAME --resamplenumber $OPTION11.CON6.RESAMPLENUMBER --numrepeat $OPTION11.CON6.NUMREPEAT --resamplenumberpercent $OPTION11.CON6.RESAMPLENUMBERPERCENT --setupgridresult $OPTION11.SETUPGRIDRESULT --setupgridecho $OPTION11.SETUPGRIDECHO --setupgridsize $OPTION11.SETUPGRIDSIZE --fitmodelresult $OPTION11.FITMODELRESULT --fitmodelecho $OPTION11.FITMODELECHO --fitmodeleval $OPTION11.FITMODELEVAL --modeldescrecho $OPTION11.MODELDESCRECHO --modeldescrresult $OPTION11.MODELDESCRRESULT --resamptableecho $OPTION11.RESAMPTABLEECHO --resamptableresult $OPTION11.RESAMPTABLERESULT --profileplotecho $OPTION11.PROFILEPLOTECHO --profileplotfig $OPTION11.PROFILEPLOTFIG --stopworkersecho $OPTION11.STOPWORKERSECHO --stopworkersresult $OPTION11.STOPWORKERSRESULT --testpredresult $OPTION11.TESTPREDRESULT --testpredecho $OPTION11.TESTPREDECHO --classprobstexresult $OPTION11.CLASSPROBSTEXRESULT --classprobstexecho $OPTION11.CLASSPROBSTEXECHO --classprobstexresult1 $OPTION11.CLASSPROBSTEXRESULT1 --classprobstexecho1 $OPTION11.CLASSPROBSTEXECHO1 --savedataecho $OPTION11.SAVEDATAECHO --savedataresult $OPTION11.SAVEDATARESULT --datasets $datasets --outputmodel $model --outputresultpdf $document;
13 #end if
14 #if $OPTION11.PARAMETERS == "basic"
15 tool2/modelBuilding.py --method $METHOD $RDATA --getdatainfoeval $OPTION11.GETDATAINFOEVAL --getdatainfoecho $OPTION11.GETDATAINFOECHO --getdatainforesult $OPTION11.GETDATAINFORESULT --missingfiltereval $OPTION11.MISSINGFILTEREVAL --missingfilterecho $OPTION11.MISSINGFILTERECHO --missingfilterresult $OPTION11.MISSINGFILTERRESULT --missingfilterthreshc $OPTION11.MISSINGFILTERTHRESHC --missingfilterthreshr $OPTION11.MISSINGFILTERTHRESHR --pcaeval $OPTION11.PCAEVAL --pcaecho $OPTION11.PCAECHO --pcaresult $OPTION11.PCARESULT --pcacomp $OPTION11.PCACOMP --pcaploteval $OPTION11.PCAPLOTEVAL --pcaplotecho $OPTION11.PCAPLOTECHO --pcaplotresult $OPTION11.PCAPLOTRESULT --pcaplotfig $OPTION11.PCAPLOTFIG --initialdataspliteval $OPTION11.INITIALDATASPLITEVAL --initialdatasplitecho $OPTION11.INITIALDATASPLITECHO --initialdatasplitresult $OPTION11.INITIALDATASPLITRESULT --saampling $OPTION11.SAAMPLING --percent $OPTION11.PERCENT --nzveval $OPTION11.NZVEVAL --nzvresult $OPTION11.NZVRESULT --nzvecho $OPTION11.NZVECHO --corrfiltereval $OPTION11.CORRFILTEREVAL --corrfilterresult $OPTION11.CORRFILTERRESULT --corrfilterecho $OPTION11.CORRFILTERECHO --threshholdcor $OPTION11.THRESHHOLDCOR --preproceval $OPTION11.PREPROCEVAL --preprocecho $OPTION11.PREPROCECHO --preprocresult $OPTION11.PREPROCRESULT --setupworkersecho $OPTION11.SETUPWORKERSECHO --setupworkersresult $OPTION11.SETUPWORKERSRESULT --numworkers $OPTION11.NUMWORKERS --setupresamplingecho $OPTION11.SETUPRESAMPLINGECHO --setupresamplingresult $OPTION11.SETUPRESAMPLINGRESULT --resampname $OPTION11.RESAMPNAME --resamplenumber $OPTION11.RESAMPLENUMBER --numrepeat $OPTION11.NUMREPEAT --resamplenumberpercent $OPTION11.RESAMPLENUMBERPERCENT --setupgridresult $OPTION11.SETUPGRIDRESULT --setupgridecho $OPTION11.SETUPGRIDECHO --setupgridsize $OPTION11.SETUPGRIDSIZE --fitmodelresult $OPTION11.FITMODELRESULT --fitmodelecho $OPTION11.FITMODELECHO --fitmodeleval $OPTION11.FITMODELEVAL --modeldescrecho $OPTION11.MODELDESCRECHO --modeldescrresult $OPTION11.MODELDESCRRESULT --resamptableecho $OPTION11.RESAMPTABLEECHO --resamptableresult $OPTION11.RESAMPTABLERESULT --profileplotecho $OPTION11.PROFILEPLOTECHO --profileplotfig $OPTION11.PROFILEPLOTFIG --stopworkersecho $OPTION11.STOPWORKERSECHO --stopworkersresult $OPTION11.STOPWORKERSRESULT --testpredresult $OPTION11.TESTPREDRESULT --testpredecho $OPTION11.TESTPREDECHO --classprobstexresult $OPTION11.CLASSPROBSTEXRESULT --classprobstexecho $OPTION11.CLASSPROBSTEXECHO --classprobstexresult1 $OPTION11.CLASSPROBSTEXRESULT1 --classprobstexecho1 $OPTION11.CLASSPROBSTEXECHO1 --savedataecho $OPTION11.SAVEDATAECHO --savedataresult $OPTION11.SAVEDATARESULT --datasets $datasets --outputmodel $model --outputresultpdf $document;
16 #end if
17
18 </command>
19 <inputs>
20 <param name="METHOD" type="select" label="SELECT METHOD FOR MODEL BUILDING" >
21 <option value="pls">Partial Least Square</option>
22 <option value="nnet">Neural Network</option>
23 <option value="bagFDA">bag-Fourier Discriminant Analysis</option>
24 <option value="blackboost">black-boost- Boosting Method</option>
25 <option value="earth">Earth-MARS based method</option>
26 <option value="rf">Random Forest</option>
27 <option value="RRF">RRFglobal -Variant of Random Forest</option>
28 <option value="svmRadial">SVM-Radial</option>
29 <option value="svmPoly">SVM-Polynomial</option>
30 <option value="ada">ada-boost</option>
31 <option value="glm">Generalised linear model </option>
32 <option value="treebag">tree based bagging method</option>
33 <option value="nb">Naive Bayes</option>
34 <option value="knn">K-nearest neighbour</option>
35 <option value="C5.0">C5.0 </option>
36 </param>
37 <param name="RDATA" format="RData" type="data" label="SELECT FILE CONATINING INPUT DATA" help="RData format" />
38
39
40 <conditional name="OPTION11">
41 <param name="PARAMETERS" type="select">
42 <option value="basic" selected="TRUE" >Use optimized parameters </option>
43 <option value="Advance"> Customized parameters </option>
44 </param>
45
46 <when value="basic">
47
48 <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" />
49
50 <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
51 <param name="GETDATAINFORESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
52
53 <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
54
55 <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
56
57 <param name="MISSINGFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
58
59 <param name="MISSINGFILTERTHRESHC" type="hidden" value="0.2" help="For column wise default is 0.2"/>
60
61 <param name="MISSINGFILTERTHRESHR" type="hidden" value="0.2" help="For row wise default is 0.2"/>
62
63 <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
64
65 <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
66
67 <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
68
69 <param name="PCACOMP" type="hidden" value="3" help="set according to need. Default is 3"/>
70
71 <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/>
72
73 <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/>
74
75 <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
76
77 <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
78
79 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
80
81 <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
82
83 <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/>
84
85 <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
86
87 <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/>
88
89 <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
90
91 <param name="NZVRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
92
93 <param name="NZVECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/>
94
95 <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
96
97 <param name="CORRFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
98
99 <param name="CORRFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
100
101 <param name="THRESHHOLDCOR" type="hidden" value="0.75" help="set according to need .default is 0.75"/>
102
103 <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
104
105 <param name="PREPROCECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
106
107 <param name="PREPROCRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
108
109 <param name="SETUPWORKERSEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. default is False"/>
110
111 <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/>
112
113 <param name="SETUPWORKERSRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
114
115 <param name="NUMWORKERS" type="hidden" value="1" help ="default is 1"/>
116
117 <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
118
119 <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
120
121 <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/>
122
123 <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/>
124
125 <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/>
126
127 <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/>
128
129 <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
130
131 <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
132
133 <param name="SETUPGRIDSIZE" type="hidden" value="3" help="default is 3 "/>
134
135 <param name="FITMODELEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
136
137 <param name="FITMODELRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
138
139 <param name="FITMODELECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
140
141 <param name="MODELDESCRECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
142
143 <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
144
145 <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
146
147 <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
148
149 <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
150
151 <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
152
153 <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
154
155 <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/>
156
157 <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/>
158
159 <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
160
161 <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
162
163 <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
164
165 <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
166
167 <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
168
169 <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
170
171 <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
172
173 </when>
174
175
176 <when value="Advance">
177 <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" />
178 <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
179 <param name="GETDATAINFORESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
180
181 <conditional name="CON1">
182 <param name="PARAMAETERS1" type="select" label="1. REMOVE MISSING VALUES FROM THE INPUT DATA">
183 <option value="YES">YES </option>
184 <option value="NO" selected="true">NO </option>
185 </param>
186
187 <when value="YES">
188 <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
189 <param name="MISSINGFILTERECHO" type="select" label="1(i). Write Code in Document" help="set True if wish to print .default is False" >
190 <option value="FALSE" selected="true">false</option>
191 <option value="TRUE">true</option>
192 </param>
193 <param name="MISSINGFILTERRESULT" type="select" label="1(ii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
194 <option value="hide">hide-result will not written in file</option>
195 <option value="tex" selected="true">tex-result will written in file</option>
196 </param>
197 <param name="MISSINGFILTERTHRESHC" type="select" label="1(iii). Set Cutoff Value for Missing Data value Columwise" help="For column wise default is 0.1 means column which has missing value more than 10% will be removed ">
198 <option value="0.1">0.1</option>
199 <option value="0.2">0.2</option>
200 <option value="0.25">0.25</option>
201 <option value="0.3">0.3</option>
202 <option value="0.35">0.35</option>
203 <option value="0.4">0.4</option>
204 <option value="0.45">0.45</option>
205 <option value="0.5">0.5</option>
206 <option value="0.55">0.55</option>
207 <option value="0.6">0.6</option>
208 <option value="0.65">0.65</option>
209 <option value="0.7">0.7</option>
210 <option value="0.75">0.75</option>
211 <option value="0.8">0.8</option>
212 </param>
213 <param name="MISSINGFILTERTHRESHR" type="select" label="1(iv). Set Cutoff Value for Missing Data Value Rowwise " help="For row wise default is 0.1 means row having more than 10% missing values will be removed">
214 <option value="0.1">0.1</option>
215 <option value="0.2">0.2</option>
216 <option value="0.25">0.25</option>
217 <option value="0.3">0.3</option>
218 <option value="0.35">0.35</option>
219 <option value="0.4">0.4</option>
220 <option value="0.45">0.45</option>
221 <option value="0.5">0.5</option>
222 <option value="0.55">0.55</option>
223 <option value="0.6">0.6</option>
224 <option value="0.65">0.65</option>
225 <option value="0.7">0.7</option>
226 <option value="0.75">0.75</option>
227 <option value="0.8">0.8</option>
228 </param>
229 </when>
230 <when value="NO">
231 <param name="MISSINGFILTEREVAL" type="hidden" value= "FALSE" help="set TRUE if wish to evaluate. default is FALSE"/>
232
233 <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
234
235 <param name="MISSINGFILTERRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
236
237 <param name="MISSINGFILTERTHRESHC" type="hidden" value="0" />
238
239 <param name="MISSINGFILTERTHRESHR" type="hidden" value="0" />
240
241 </when>
242 </conditional>
243
244 <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
245
246 <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
247
248 <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
249
250 <param name="PCACOMP" type="select" label="2. FIND NUMBER OF PRINCIPLE COMPONENT" help="performs PCA and gives number of PC. Default is 3 ">
251 <option value="3">3</option>
252 <option value="4">4</option>
253 <option value="5">5</option>
254 <option value="6">6</option>
255 <option value="7">7</option>
256 <option value="8">8</option>
257 <option value="9">9</option>
258 <option value="10">10</option>
259 </param>
260
261 <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/>
262
263 <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/>
264
265 <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
266
267 <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
268
269
270 <conditional name="CON2">
271 <param name="PARAMAETERS2" type="select" label="3. CUSTOMIZE PARAMETERS FOR DATA SPLITTING " help="splits data in test and train set.">
272 <option value="YES2">YES </option>
273 <option value="NO2" selected="true">NO </option>
274 </param>
275 <when value="YES2">
276 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
277 <param name="SAAMPLING" type="select" label="3(i). Select Sampling Method" help="Defualt is with No sampling. you may choose downsample or upsample" >
278 <option value="garBage" selected="true">No Sampling</option>
279 <option value="downsampling">downsample</option>
280 <option value="upsampling">upsample</option>
281 </param>
282 <param name="INITIALDATASPLITECHO" type="select" label="3(ii). Write Code in Document" help="set True if wish to print .default is False" >
283 <option value="FALSE">false</option>
284 <option value="TRUE">true</option>
285 </param>
286 <param name="INITIALDATASPLITRESULT" type="select" value="tex" label="3(iii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
287 <option value="tex" selected="true">tex-result will written in file</option>
288 <option value="hide">hide-result will not written in file</option>
289 </param>
290 <param name="PERCENT" type="select" label="3(iv) .Set Value at Which Data Will be Splitted in Train and Test Set" help="default is 0.8">
291 <option value="0.8">0.8</option>
292 <option value="0.75">0.75</option>
293 <option value="0.6">0.6</option>
294 <option value="0.5">0.5</option>
295 <option value="2">use entire data set</option>
296 </param>
297 </when>
298 <when value="NO2">
299 <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/>
300
301 <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
302
303 <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/>
304
305 <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
306
307 <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/>
308
309 </when>
310 </conditional>
311
312 <conditional name="CON3">
313 <param name="PARAMAETERS3" type="select" label="4. REMOVE NEAR ZERO VARIANCE " help="removes NZV from train and test set.">
314 <option value="YES3">YES </option>
315 <option value="NO3" selected="true">NO </option>
316 </param>
317 <when value="YES3">
318
319 <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
320
321
322 <param name="NZVECHO" type="select" label="4(i). Write Code in Document" help="set True if wish to print .default is False">
323 <option value="FALSE">false</option>
324 <option value="TRUE">true</option>
325 </param>
326
327 <param name="NZVRESULT" type="select" label="4(ii). Write Result in document" help="Set tex if wish to write result in output pdf file. default is tex">
328 <option value="hide">hide-result will not written in file</option>
329 <option value="tex" selected="true">tex-result will written in file</option>
330 </param>
331 </when>
332 <when value="NO3">
333 <param name="NZVEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/>
334 <param name="NZVECHO" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/>
335 <param name="NZVRESULT" type="hidden" value="hide" help="set TRUE if wish to evaluate."/>
336 </when>
337 </conditional>
338
339 <!--param name="NZVECHO" type="select" label="Write Code in Document" help="set True if wish to print .default is False">
340 <option value="FALSE">false</option>
341 <option value="TRUE">true</option>
342 </param-->
343
344 <conditional name="CON4">
345 <param name="PARAMAETERS4" type="select" label="5. REMOVE CORRELATED VALUES" help="removes correlated attributes from train and test set.">
346 <option value="YES4">YES </option>
347 <option value="NO4" selected="true">NO </option>
348 </param>
349 <when value="YES4">
350 <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
351 <param name="THRESHHOLDCOR" type="select" label="5(i). cutoff for correlated Value " help="set according to need .default is 0.75 means attributes have 75% or more correlation are ommited from the data">
352 <option value="0.75">0.75</option>
353 <option value="0.4">0.4</option>
354 <option value="0.45">0.45</option>
355 <option value="0.5">0.5</option>
356 <option value="0.55">0.55</option>
357 <option value="0.6">0.6</option>
358 <option value="0.65">0.65</option>
359 <option value="0.7">0.7</option>
360 <option value="0.8">0.8</option>
361 <option value="0.85">0.85</option>
362 <option value="0.9">0.9</option>
363 <option value="0.95">0.95</option>
364 </param>
365 <param name="CORRFILTERECHO" type="select" label="5(ii). Write Code in Document" help="set True if wish to print .default is False" >
366 <option value="FALSE">false</option>
367 <option value="TRUE">true</option>
368 </param>
369 <param name="CORRFILTERRESULT" type="select" label="5(iii). Write Result in document" help="Set tex if wish to write in output pdf file. default is tex">
370 <option value="hide">hide-result will not written in file</option>
371 <option value="tex" selected="true">tex-result will written in file</option>
372 </param>
373 </when>
374 <when value="NO4">
375 <param name="CORRFILTEREVAL" type="hidden" value="FALSE"/>
376
377 <param name="CORRFILTERRESULT" type="hidden" value="hide" />
378
379 <param name="CORRFILTERECHO" type="hidden" value="FALSE" />
380
381 <param name="THRESHHOLDCOR" type="hidden" value="0" />
382 </when>
383 </conditional>
384
385 <conditional name="CON5">
386 <param name="PARAMAETERS5" type="select" label="6. PERFORM CENTERING AND SCALING OF DATA " help="centering and scaling of train and test set.">
387 <option value="YES5">YES </option>
388 <option value="NO5" selected="true">NO </option>
389 </param>
390
391 <when value="YES5">
392 <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
393 <param name="PREPROCECHO" type="select" label="6(i). Write Code in Document" help="set True if wish to write code in document .default is False" >
394 <option value="FALSE">false</option>
395 <option value="TRUE">true</option>
396 </param>
397 <param name="PREPROCRESULT" type="select" label="6(ii). Write Result in document " help="Set tex if wish to write result in output pdf file. default is tex">
398 <option value="hide">hide-result will not written in file</option>
399 <option value="tex" selected="true">tex-result will written in file</option>
400 </param>
401 </when>
402 <when value="NO5">
403 <param name="PREPROCEVAL" type="hidden" value="FALSE"/>
404
405 <param name="PREPROCECHO" type="hidden" value="FALSE" />
406
407 <param name="PREPROCRESULT" type="hidden" value="hide" />
408
409 </when>
410 </conditional>
411
412 <param name="SETUPWORKERSEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is False"/>
413 <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
414 <param name="NUMWORKERS" type="select" label="7. SET NUMBER OF PROCESSORS " help ="default is 1">
415 <option value="1">1</option>
416 <option value="2">2</option>
417 <option value="4">4</option>
418 <option value="6">6</option>
419 <option value="8">8</option>
420 <option value="16">16</option>
421 </param>
422 <param name="SETUPWORKERSRESULT" type="hidden" value="hide" />
423
424 <conditional name="CON6">
425
426 <param name="PARAMAETERS6" type="select" label="8. CUSTOMIZE RESAMPLING PARAMETERS" help="resampling for cross validation">
427 <option value="YES6">YES </option>
428 <option value="NO6" selected="true">NO </option>
429 </param>
430 <when value="YES6">
431 <param name="SETUPRESAMPLINGECHO" type="select" label="8(i). write code for resampling" help="set True if wish to print .default is False">
432 <option value="FALSE">false</option>
433 <option value="TRUE">true</option>
434 </param>
435 <param name="SETUPRESAMPLINGRESULT" type="select" label="8(ii). Write Result in document " help="Set tex if wish to write in output pdf file. default is hide">
436 <option value="hide">hide-result will not written in file</option>
437 <option value="tex">tex-result will written in file</option>
438 </param>
439
440
441 <param name="RESAMPNAME" type="select" label="8(iii). select Resample method for cross validation" help="default is boot632 ">
442 <option value="boot632" selected="true">boot632</option>
443 <option value="boot">boot</option>
444 <option value="cv">cv</option>
445 <option value="repeatedcv">repeatedcv</option>
446 <option value="LOOCV">LOOCV - leave one out</option>
447 </param>
448
449 <param name="RESAMPLENUMBER" type="select" label="8(iv). Set Number of times Resample" help="default is 10 ">
450 <option value="10" selected="true">10</option>
451 <option value="5">5</option>
452 <option value="15">15</option>
453 <option value="20">20</option>
454 <option value="25">25</option>
455 </param>
456
457 <param name="NUMREPEAT" type="select" label="8(v). Set Number of times to repeat" help="default is 3 ">
458 <option value="3" selected="true">3</option>
459 <option value="1">1</option>
460 <option value="5">5</option>
461 <option value="10">10</option>
462 </param>
463 <param name="RESAMPLENUMBERPERCENT" type="select" label="8(vi). Set Percent splitting of data for resampling" help="default is 0.75">
464 <option value="0.75" selected="true">0.75</option>
465 <option value="0.4">0.4</option>
466 <option value="0.45">0.45</option>
467 <option value="0.5">0.5</option>
468 <option value="0.55">0.55</option>
469 <option value="0.6">0.6</option>
470 <option value="0.65">0.65</option>
471 <option value="0.7">0.7</option>
472 <option value="0.8">0.8</option>
473 </param>
474 </when>
475 <when value="NO6">
476
477 <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
478
479 <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
480
481 <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/>
482
483 <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/>
484
485 <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/>
486
487 <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/>
488
489
490 </when>
491 </conditional>
492 <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
493
494 <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
495
496 <param name="SETUPGRIDSIZE" type="select" label="9. SET SIZE OF GRID" help="default is 3 ">
497 <option value="3">3</option>
498 <option value="4">4</option>
499 <option value="5">5</option>
500 <option value="6">6</option>
501 <option value="7">7</option>
502 <option value="8">8</option>
503 <option value="9">9</option>
504 <option value="10">10</option>
505 <option value="11">11</option>
506 <option value="12">12</option>
507 <option value="13">13</option>
508 <option value="14">14</option>
509 <option value="15">15</option>
510 <option value="16">16</option>
511 <option value="17">17</option>
512 <option value="18">18</option>
513 <option value="19">19</option>
514 <option value="20">20</option>
515 </param>
516
517 <param name="FITMODELEVAL" type="boolean" checked="true" value="true" label="10. BUILD A MODEL AND WRITE RESULT IN DOCUMENT" help="default is TRUE"/>
518 <param name="FITMODELRESULT" type="hidden" value="tex" />
519 <param name="FITMODELECHO" type="select" label="10(i). Write Code for model building in Document" help="set True if wish to write code in document .default is False" >
520 <option value="FALSE">false</option>
521 <option value="TRUE">true</option>
522 </param>
523 <param name="MODELDESCRECHO" type="select" label="10(ii). Write code for Model Description " help="set True if wish to print .default is False" >
524 <option value="FALSE">false</option>
525 <option value="TRUE">true</option>
526 </param>
527 <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
528
529 <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
530
531 <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
532
533 <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
534
535 <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/>
536
537 <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
538
539 <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/>
540
541 <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/>
542
543 <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/>
544
545 <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
546
547 <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
548
549 <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/>
550
551 <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" />
552
553 <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/>
554
555 <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/>
556
557 </when>
558 </conditional>
559 </inputs>
560
561 <outputs>
562 <data format="RData" label="$METHOD Model" name="model" />
563 <data format="pdf" label="Document for $METHOD" name="document" />
564 <data format="RData" label="Datasets used for model building " name="datasets" />
565 </outputs>
566 <help>
567
568 .. class:: infomark
569
570
571
572 **Instruction**
573
574 ----------
575
576 Users may change any parameter as their requirement. For normal practice
577
578 user required to provide only input csv file and method for model building.
579
580 More details are given in user manual.Please click here
581
582
583
584
585 </help>
586
587
588
589 </tool>