annotate evaluate_aggregation.xml @ 100:09827a9f75a6 draft

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<tool id="aggregEval" name="aggregation_evaluation" version="1.0.0">
  <description>tool to evaluate aggregation accuracy</description>
  <command interpreter="Rscript">
	 evaluate_aggregation.R $config &gt; ${output1}
  </command>
  
  <inputs>
	 
	 <param name="genotype" type="data"
		label="genotype data" help="path to a file containing the encoded genotypes" 
		/> 
	 
	<param name="lasso" type="data" optional="true"
		label="lasso model" help="path to rds containing LASSO model" 
	/>
	
	<param name="rf" type="data" optional="true"
		label="rf model" help="path to rds containing Random Forest model" 
		/>
		
	<param name="rrBLUP" type="data" optional="true"
		label="rrBLUP model" help="path to rds containing rrBLUP model" 
		/>
		
	<param name="svm" type="data" optional="true"
		label="SVM model" help="path to rds containing SVM model" 
		/>
		  
	<param name="phenotype" type="data"
			label="phenotype data" help=" a tabular datatype containing the phenotypes " 
			/>
			
	<param name="folds" type="data"
			label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " 
			/>
	<param name="method" type="text" value="svm"
			label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm" 
			/>
	<param name="kernel" type="text" value="linear"
			label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid" 
			/>		
	
  </inputs>
  
  <configfiles>
    <configfile name="config">
## Desc: this file is sourced in encode wrapper script
##  as means to pass all galaxy params to R
"${genotype}" -> genotype
"${lasso}" -> lassoModel
"${rf}" -> rfModel
"${rrBLUP}" -> rrBLUPModel
"${svm}" -> svmModel
"${phenotype}" -> phenotype
"${output1}" -> out
"${folds}" -> folds
"${method}" -> method
"${kernel}" -> kernel

    </configfile>
</configfiles>
  
<outputs>
	<data format="tabular" name = "output1" label="aggregation evaluation" />
</outputs>
  
  <help>
	  
  </help>
  </tool>