<tool id="qualityControl" name="qualityControl" version="1.0.0">
  <description>perform QC on a dataset</description>
  <command interpreter="Rscript">
	  qualityControl.R $config &gt; ${reportPath}
  </command>
  
  <inputs>
	<param name="genotype" type="data"
		label="genotype data" help="genotype must be a .csv" 
	/>
		  
	<param name="plinkFreq" type="data"
			  label="plink files with frequencies" help="" 
	/>
	
	<param name="plinkHWE" type="data"
		label="plink files with HardyWeinberg statistics" help=""  
	/>
  </inputs>
  
  
    <configfiles>
    <configfile name="config">
## Desc: this file is sourced in encode wrapper script
##  as means to pass all galaxy params to R
"${genotype}" -> genotype
"${plinkFreq}" -> plinkFreq
"${plinkHWE}" -> plinkHWE
"${reportPath}" -> out

    </configfile>
</configfiles>
  
<outputs>
	<data format="plain text" name="reportPath" label="QC report" />
</outputs>
  
  <help>
	  make a report with dimension of the dataset, MAF, Hardy-Weinberg test
  </help>
  </tool>