annotate aggregation.xml @ 78:5a56e1e3b235 draft

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<tool id="aggreg" name="aggregation" version="1.0.0">
  <description>predict phenotype by combining multiple classifiers</description>
  <command interpreter="Rscript">
	  aggregation.R $config &gt; ${output1}
  </command>
  
  <inputs>
	<param name="lassoPred" type="data" optional="true"
		label="lasso prediction" help="path to rds containing LASSO prediction" 
	/>
	
	<param name="rfPred" type="data" optional="true"
		label="rf prediction" help="path to rds containing Random Forest prediction" 
		/>
		
	<param name="rrBLUPPred" type="data" optional="true"
		label="rrBLUP prediction" help="path to rds containing rrBLUP prediction" 
		/>
		
	<param name="svmPred" type="data" optional="true"
		label="SVM prediction" help="path to rds containing SVM prediction" 
		/>
		  
	<param name="phenotype" type="data"
			label="phenotype data" help=" a tabular datatype containing the phenotypes " 
			/>
	
	<param name="eval" type="integer" value="0"
			label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model " 
			/>
			
	<param name="folds" type="data" optional="true"
			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="model" type="data" optional="true"
			label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen" 
			/>
	<!-- deprecated <param name="out" type="text"
			label="output path" help= " a path to a rds file" -->
			/>
	<param name="method" type="text" value="svm"
			label="aggregation method" help= "choose among geneticMean, rrBLUP, 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
"${lassoPred}" -> lassoPred
"${rfPred}" -> rfPred
"${rrBLUPPred}" -> rrBLUPPred
"${svmPred}" -> svmPred
"${phenotype}" -> phenotype
"${model}" -> model
"${output1}" -> out
"${eval}" -> evaluation
"${folds}" -> folds
"${method}" -> method
"${kernel}" -> kernel
"${eval}" -> doEvaluation

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