annotate model_building.xml @ 1:247d404ffbcf draft default tip

planemo upload commit e1c7666c1ed218d9b273dc3aeb1b6b765f351324-dirty

<tool id="rcaret_classification_model" name="R-Caret Classifcation Model-Builder" version="1.0">
	<description>builds 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 input data file" 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>