<tool id="evaluation" name="evaluation" version="1.0.0">
  <description>evaluate results of classifiers prediction</description>
  <command interpreter="Rscript">
	  evaluation.R $config &gt; ${output1}
  </command>
  
  <inputs>
	<param name="genotype" type="data"
		label="genotype data" 
	/>
	
	<param name="prediction" type="data"
		label="results of prediction" 
	/>
		  
	<param name="phenotype" type="data"
			label="phenotype file" 
	/>
	
	<param name="r2" type="integer" value="1"
			label="compute r-squared distance" help=" whether or not to compute the r-squared distance. 1 means the tool will compute it, any other argument means it will not be computed " 
	/>
	
	<param name="cor" type="integer" value="1"
			label="compute correlation" help=" whether or not to compute the correlation between predictions and ture values. 1 means the tool will compute it, any other argument means it will not be computed " 
	/>
	
	<param name="folds" type="data"
			label="folds" help=" path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. " 
	/>
	
  </inputs>
  
  
 <configfiles>
    <configfile name="config">
## Desc: this file is sourced in encode wrapper script
##  as means to pass all galaxy params to R
"${genotype}" -> genotype
"${phenotype}" -> phenotype
"${prediction}" -> prediction
"${r2}" -> doR2
"${cor}" -> doCor
"${folds}" -> folds
    </configfile>
</configfiles>
  
<outputs>
	<data format="tabular" name = "output1" label="classifier prediction" />
</outputs>  

  <help>
	  evaluate the predictions of classifiers. For now correlation between true valeus and predictions, and r-squared distance are implemeted
  </help>
  </tool>