Mercurial > repos > anmoljh > rcaret_classification_model
diff model_building.xml @ 0:2cb81da69c73 draft
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272
| author | anmoljh |
|---|---|
| date | Thu, 31 May 2018 11:58:59 -0400 |
| parents | |
| children | 247d404ffbcf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/model_building.xml Thu May 31 11:58:59 2018 -0400 @@ -0,0 +1,511 @@ +<tool id="rcaret_classification_model" name="R-Caret Classifcation Model-Builder" version="1.0"> + <description>Build r-caret package based classification models</description> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.0">carettools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + +<command interpreter="python"> +#if $OPTION11.PARAMETERS == "Advance" +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; +#end if +#if $OPTION11.PARAMETERS == "basic" +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; +#end if +</command> + +<inputs> + <param name="METHOD" type="select" label="SELECT METHOD FOR MODEL BUILDING" > + <option value="pls">Partial Least Square</option> + <option value="nnet">Neural Network</option> + <option value="bagFDA">bag-Fourier Discriminant Analysis</option> + <!--option value="blackboost">black-boost- Boosting Method</option--> + <option value="earth">Earth-MARS based method</option> + <option value="rf">Random Forest</option> + <option value="RRF">RRFglobal -Variant of Random Forest</option> + <option value="svmRadial">SVM-Radial</option> + <option value="svmPoly">SVM-Polynomial</option> + <option value="ada">ada-boost</option> + <option value="glm">Generalised linear model </option> + <option value="treebag">tree based bagging method</option> + <option value="nb">Naive Bayes</option> + <option value="knn">K-nearest neighbour</option> + <option value="C5.0">C5.0 </option> + </param> + <param name="RDATA" type="data" format="rdata" label="SELECT FILE CONATINING INPUT DATA" help="RData/RDS format" /> + + + <conditional name="OPTION11"> + <param name="PARAMETERS" type="select"> + <option value="basic" selected="True" >Use optimized parameters </option> + <option value="Advance"> Customized parameters </option> + </param> + + <when value="basic"> + + <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" /> + <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="GETDATAINFORESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="MISSINGFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="MISSINGFILTERTHRESHC" type="hidden" value="0.2" help="For column wise default is 0.2"/> + <param name="MISSINGFILTERTHRESHR" type="hidden" value="0.2" help="For row wise default is 0.2"/> + <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="PCACOMP" type="hidden" value="3" help="set according to need. Default is 3"/> + <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/> + <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/> + <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/> + <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/> + <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/> + <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="NZVRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="NZVECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/> + <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="CORRFILTERRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="CORRFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="THRESHHOLDCOR" type="hidden" value="0.75" help="set according to need .default is 0.75"/> + <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="PREPROCECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="PREPROCRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="SETUPWORKERSEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. default is False"/> + <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" label="Write Code in Document" help="set True if wish to print .default is False"/> + <param name="SETUPWORKERSRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="NUMWORKERS" type="hidden" value="1" help ="default is 1"/> + <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/> + <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/> + <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/> + <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/> + <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SETUPGRIDSIZE" type="hidden" value="3" help="default is 3 "/> + <param name="FITMODELEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="FITMODELRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="FITMODELECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="MODELDESCRECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" /> + <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" /> + <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + </when> + + <when value="Advance"> + <param name="GETDATAINFOEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE" /> + <param name="GETDATAINFOECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="GETDATAINFORESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + + <conditional name="CON1"> + <param name="PARAMAETERS1" type="select" label="1. REMOVE MISSING VALUES FROM THE INPUT DATA"> + <option value="YES">YES </option> + <option value="NO" selected="true">NO </option> + </param> + + <when value="YES"> + <param name="MISSINGFILTEREVAL" type="hidden" value= "TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="MISSINGFILTERECHO" type="select" label="1(i). Write Code in Document" help="set True if wish to print .default is False" > + <option value="FALSE" selected="true">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="hide">hide-result will not written in file</option> + <option value="tex" selected="true">tex-result will written in file</option> + </param> + <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 "> + <option value="0.1">0.1</option> + <option value="0.2">0.2</option> + <option value="0.25">0.25</option> + <option value="0.3">0.3</option> + <option value="0.35">0.35</option> + <option value="0.4">0.4</option> + <option value="0.45">0.45</option> + <option value="0.5">0.5</option> + <option value="0.55">0.55</option> + <option value="0.6">0.6</option> + <option value="0.65">0.65</option> + <option value="0.7">0.7</option> + <option value="0.75">0.75</option> + <option value="0.8">0.8</option> + </param> + <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"> + <option value="0.1">0.1</option> + <option value="0.2">0.2</option> + <option value="0.25">0.25</option> + <option value="0.3">0.3</option> + <option value="0.35">0.35</option> + <option value="0.4">0.4</option> + <option value="0.45">0.45</option> + <option value="0.5">0.5</option> + <option value="0.55">0.55</option> + <option value="0.6">0.6</option> + <option value="0.65">0.65</option> + <option value="0.7">0.7</option> + <option value="0.75">0.75</option> + <option value="0.8">0.8</option> + </param> + </when> + + <when value="NO"> + <param name="MISSINGFILTEREVAL" type="hidden" value= "FALSE" help="set TRUE if wish to evaluate. default is FALSE"/> + <param name="MISSINGFILTERECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="MISSINGFILTERRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="MISSINGFILTERTHRESHC" type="hidden" value="0" /> + <param name="MISSINGFILTERTHRESHR" type="hidden" value="0" /> + + </when> + </conditional> + + <param name="PCAEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="PCAECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="PCARESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="PCACOMP" type="select" label="2. FIND NUMBER OF PRINCIPLE COMPONENT" help="performs PCA and gives number of PC. Default is 3 "> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + <option value="10">10</option> + </param> + <param name="PCAPLOTEVAL" type="hidden" value="TRUE" help="set TRUE if wish to plot PCA. default is TRUE"/> + <param name="PCAPLOTECHO" type="hidden" value="FALSE" help="Set True if wish to Print .default is False"/> + <param name="PCAPLOTRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PCAPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + + <conditional name="CON2"> + <param name="PARAMAETERS2" type="select" label="3. CUSTOMIZE PARAMETERS FOR DATA SPLITTING " help="splits data in test and train set."> + <option value="YES2">YES </option> + <option value="NO2" selected="true">NO </option> + </param> + + <when value="YES2"> + <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/> + <param name="SAAMPLING" type="select" label="3(i). Select Sampling Method" help="Defualt is with No sampling. you may choose downsample or upsample" > + <option value="garBage" selected="true">No Sampling</option> + <option value="downsampling">downsample</option> + <option value="upsampling">upsample</option> + </param> + <param name="INITIALDATASPLITECHO" type="select" label="3(ii). Write Code in Document" help="set True if wish to print .default is False" > + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="tex" selected="true">tex-result will written in file</option> + <option value="hide">hide-result will not written in file</option> + </param> + <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"> + <option value="0.8">0.8</option> + <option value="0.75">0.75</option> + <option value="0.6">0.6</option> + <option value="0.5">0.5</option> + <option value="2">use entire data set</option> + </param> + </when> + + <when value="NO2"> + <param name="INITIALDATASPLITEVAL" type="hidden" value= "TRUE" help="set TRUE for splitting in test and train set.default is True"/> + <param name="INITIALDATASPLITECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SAAMPLING" type="hidden" value="garBage" help="default is with No sampling"/> + <param name="INITIALDATASPLITRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PERCENT" type="hidden" value="0.8" help="default is 0.8"/> + </when> + </conditional> + + <conditional name="CON3"> + <param name="PARAMAETERS3" type="select" label="4. REMOVE NEAR ZERO VARIANCE " help="removes NZV from train and test set."> + <option value="YES3">YES </option> + <option value="NO3" selected="true">NO </option> + </param> + + <when value="YES3"> + <param name="NZVEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="NZVECHO" type="select" label="4(i). Write Code in Document" help="set True if wish to print .default is False"> + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="hide">hide-result will not written in file</option> + <option value="tex" selected="true">tex-result will written in file</option> + </param> + </when> + + <when value="NO3"> + <param name="NZVEVAL" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/> + <param name="NZVECHO" type="hidden" value="FALSE" help="set TRUE if wish to evaluate. "/> + <param name="NZVRESULT" type="hidden" value="hide" help="set TRUE if wish to evaluate."/> + </when> + </conditional> + + <!--param name="NZVECHO" type="select" label="Write Code in Document" help="set True if wish to print .default is False"> + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param--> + + <conditional name="CON4"> + <param name="PARAMAETERS4" type="select" label="5. REMOVE CORRELATED VALUES" help="removes correlated attributes from train and test set."> + <option value="YES4">YES </option> + <option value="NO4" selected="true">NO </option> + </param> + + <when value="YES4"> + <param name="CORRFILTEREVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <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"> + <option value="0.75">0.75</option> + <option value="0.4">0.4</option> + <option value="0.45">0.45</option> + <option value="0.5">0.5</option> + <option value="0.55">0.55</option> + <option value="0.6">0.6</option> + <option value="0.65">0.65</option> + <option value="0.7">0.7</option> + <option value="0.8">0.8</option> + <option value="0.85">0.85</option> + <option value="0.9">0.9</option> + <option value="0.95">0.95</option> + </param> + <param name="CORRFILTERECHO" type="select" label="5(ii). Write Code in Document" help="set True if wish to print .default is False" > + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="hide">hide-result will not written in file</option> + <option value="tex" selected="true">tex-result will written in file</option> + </param> + </when> + + <when value="NO4"> + <param name="CORRFILTEREVAL" type="hidden" value="FALSE"/> + <param name="CORRFILTERRESULT" type="hidden" value="hide" /> + <param name="CORRFILTERECHO" type="hidden" value="FALSE" /> + <param name="THRESHHOLDCOR" type="hidden" value="0" /> + </when> + </conditional> + + <conditional name="CON5"> + <param name="PARAMAETERS5" type="select" label="6. PERFORM CENTERING AND SCALING OF DATA " help="centering and scaling of train and test set."> + <option value="YES5">YES </option> + <option value="NO5" selected="true">NO </option> + </param> + + <when value="YES5"> + <param name="PREPROCEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <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" > + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="hide">hide-result will not written in file</option> + <option value="tex" selected="true">tex-result will written in file</option> + </param> + </when> + + <when value="NO5"> + <param name="PREPROCEVAL" type="hidden" value="FALSE"/> + <param name="PREPROCECHO" type="hidden" value="FALSE" /> + <param name="PREPROCRESULT" type="hidden" value="hide" /> + </when> + + </conditional> + + <param name="SETUPWORKERSEVAL" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is False"/> + <param name="SETUPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" /> + <param name="NUMWORKERS" type="select" label="7. SET NUMBER OF PROCESSORS " help ="default is 1"> + <option value="1">1</option> + <option value="2">2</option> + <option value="4">4</option> + <option value="6">6</option> + <option value="8">8</option> + <option value="16">16</option> + </param> + <param name="SETUPWORKERSRESULT" type="hidden" value="hide" /> + + <conditional name="CON6"> + <param name="PARAMAETERS6" type="select" label="8. CUSTOMIZE RESAMPLING PARAMETERS" help="resampling for cross validation"> + <option value="YES6">YES </option> + <option value="NO6" selected="true">NO </option> + </param> + + <when value="YES6"> + <param name="SETUPRESAMPLINGECHO" type="select" label="8(i). write code for resampling" help="set True if wish to print .default is False"> + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <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"> + <option value="hide">hide-result will not written in file</option> + <option value="tex">tex-result will written in file</option> + </param> + + <param name="RESAMPNAME" type="select" label="8(iii). select Resample method for cross validation" help="default is boot632 "> + <option value="boot632" selected="true">boot632</option> + <option value="boot">boot</option> + <option value="cv">cv</option> + <option value="repeatedcv">repeatedcv</option> + <option value="LOOCV">LOOCV - leave one out</option> + </param> + + <param name="RESAMPLENUMBER" type="select" label="8(iv). Set Number of times Resample" help="default is 10 "> + <option value="10" selected="true">10</option> + <option value="5">5</option> + <option value="15">15</option> + <option value="20">20</option> + <option value="25">25</option> + </param> + + <param name="NUMREPEAT" type="select" label="8(v). Set Number of times to repeat" help="default is 3 "> + <option value="3" selected="true">3</option> + <option value="1">1</option> + <option value="5">5</option> + <option value="10">10</option> + </param> + + <param name="RESAMPLENUMBERPERCENT" type="select" label="8(vi). Set Percent splitting of data for resampling" help="default is 0.75"> + <option value="0.75" selected="true">0.75</option> + <option value="0.4">0.4</option> + <option value="0.45">0.45</option> + <option value="0.5">0.5</option> + <option value="0.55">0.55</option> + <option value="0.6">0.6</option> + <option value="0.65">0.65</option> + <option value="0.7">0.7</option> + <option value="0.8">0.8</option> + </param> + </when> + + <when value="NO6"> + <param name="SETUPRESAMPLINGECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SETUPRESAMPLINGRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="RESAMPNAME" type="hidden" value="boot632" label="Set type of resampling for cross validation" help="default is boot632"/> + <param name="RESAMPLENUMBER" type="hidden" value="10" label="Set Number of Times to Resample" help="default is 10"/> + <param name="NUMREPEAT" type="hidden" value="3" label="Set Number of Times to run" help="default is 3"/> + <param name="RESAMPLENUMBERPERCENT" type="hidden" value="0.75" help="default is 0.75"/> + </when> + + </conditional> + + <param name="SETUPGRIDRESULT" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="SETUPGRIDECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SETUPGRIDSIZE" type="select" label="9. SET SIZE OF GRID" help="default is 3 "> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + <option value="10">10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15">15</option> + <option value="16">16</option> + <option value="17">17</option> + <option value="18">18</option> + <option value="19">19</option> + <option value="20">20</option> + </param> + + <param name="FITMODELEVAL" type="boolean" checked="true" value="true" label="10. BUILD A MODEL AND WRITE RESULT IN DOCUMENT" help="default is TRUE"/> + <param name="FITMODELRESULT" type="hidden" value="tex" /> + <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" > + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <param name="MODELDESCRECHO" type="select" label="10(ii). Write code for Model Description " help="set True if wish to print .default is False" > + <option value="FALSE">false</option> + <option value="TRUE">true</option> + </param> + <param name="MODELDESCRRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="RESAMPTABLEECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="RESAMPTABLERESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="PROFILEPLOTECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="PROFILEPLOTFIG" type="hidden" value="TRUE" help="set TRUE if wish to evaluate. default is TRUE"/> + <param name="STOPWORKERSECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="STOPWORKERSRESULT" type="hidden" value= "hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="TESTPREDRESULT" type="hidden" value= "tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="TESTPREDECHO" type="hidden" value="FALSE" help="set True if wish to print. default is False"/> + <param name="CLASSPROBSTEXRESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + <param name="CLASSPROBSTEXECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False" /> + <param name="CLASSPROBSTEXRESULT1" type="hidden" value="hide" help="Set tex if wish to write in output pdf file. default is hide"/> + <param name="CLASSPROBSTEXECHO1" type="hidden" value="FALSE" help="set True if wish to print .default is False" /> + <param name="SAVEDATAECHO" type="hidden" value="FALSE" help="set True if wish to print .default is False"/> + <param name="SAVEDATARESULT" type="hidden" value="tex" help="Set tex if wish to write in output pdf file. default is tex"/> + + </when> + </conditional> +</inputs> + +<outputs> + <data format="rdata" label="$METHOD Model" name="model" /> + <data format="pdf" label="Document for $METHOD" name="document" /> + <data format="rdata" label="Datasets used for model building " name="datasets" /> +</outputs> + +<help> + +.. class:: infomark + + + +**Instruction** + +---------- + +Users may change any parameter as their requirement. For normal practice + +user required to provide only input csv file and method for model building. + +More details are given in user manual.Please click here + + +</help> +<tests> + <test> + <param name="METHOD" value="pls" /> + <param name="RDATA" value="desc.rdata"/> + <param name="PARAMETERS" value="basic" /> + <output name="model" file="MODEL.rdata" compare="sim_size" delta="20000" /> + <output name="datasets" file="datasets.rdata" compare="sim_size" delta="20000" /> + <output name="document" file="MODEL.pdf" compare="sim_size" delta="2000000" > + <!--extra_files type="file" name="cmd.log.1" value="test2/cmd.log.1" compare="sim_size" delta="20000"/> + <extra_files type="file" name="cmd.log.2" value="test2/cmd.log.2" compare="sim_size" delta="20000"/> + <extra_files type="file" name="dataset_2.dat" value="test2/dataset_2.dat" compare="sim_size" delta="80000"/> + <extra_files type="file" name="dtaset_3.dat" value="test2/dtaset_3.dat" compare="sim_size" delta="80000"/--> + <extra_files type="file" name="obsPred.pdf" value="test2/obsPred.pdf" compare="sim_size" delta="80000" /> + <extra_files type="file" name="result-doc.aux" value="test2/result-doc.aux" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc-densityplot.pdf" value="test2/result-doc-densityplot.pdf" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc.log" value="test2/result-doc.log" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc.out" value="test2/result-doc.out" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc-pcaPlot.pdf" value="test2/result-doc-pcaPlot.pdf" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc.pdf" value="test2/result-doc.pdf" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc-profilePlot.pdf" value="test2/result-doc-profilePlot.pdf" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc.Rnw" value="test2/result-doc.Rnw" compare="sim_size" delta="80000"/> + <extra_files type="file" name="result-doc.tex" value="test2/result-doc.tex" compare="sim_size" delta="80000"/> + <!--extra_files type="file" name="pls-Fit.RData" value="test2/pls-Fit.RData" compare="sim_size" delta="9000000"/--> + </output> + </test> +</tests> + +</tool>