<tool id="optimizer" name="optimizer" version="1">
  <description> Optimizer</description>
  <requirements>
    <requirement type="package" >perl</requirement>
    <requirement type="package" >r-base</requirement>
  </requirements>
  <command> <![CDATA[
	ln -s $__tool_directory__/score_complete_alt.pl 2>$log &&
	ln -s $__tool_directory__/wilcox.R 2>>$log &&
	ln -s $fileR fileR &&
	ln -s $fileC fileC &&
	



	perl $__tool_directory__/optimizer.pl


	###INPUT VCF FILE	
	
	-fileR fileR -fileC fileC


 
	 
	#if $qfile
        -leQTL $qfile
        #else
        -leQTL $__tool_directory__/qfile
        #end if
        
	#if $similarD
        -similarD $similarD
        #end if
	
	#if $disease
        -disease $disease
        #end if
	
	#if $lgenes
        -lgenes $lgenes
        #end if
	 
        #if $kfile      
        -keywords $kfile
        #else
        -keywords $__tool_directory__/kfile 
        #end if
	
	#if $efile
        -effects $efile
        #else
        -effects $__tool_directory__/efile
        #end if


	###RANGE VALUES
	-disease_clinvar $disease_clinvarMIN:$disease_clinvarMAX
	
	-score_AF $score_AFMIN:$score_AFMAX
	
	-score_functional $score_functionalMIN:$score_functionalMAX
	
	-score_NS $score_NSMIN:$score_NSMAX
	
	-score_nIND $score_nINDMIN:$score_nINDMAX
	
	-AF $AF 
	
	-scoreeQTL $scoreeQTLMIN:$scoreeQTLMAX	
	
	-scoreG $scoreGMIN:$scoreGMAX
	-nind $nind 
	
	###OUTPUT
	-ofile $ofile
 	
	2>>$log



    ]]>
  </command>
  <inputs>
    <param format="vcf" name="fileR" type="data" label="VCF" help="vcf fileR test ALL input file"/>
    <param format="vcf" name="fileC" type="data" label="VCF" help="vcf fileC test test_unefected input file"/>
<!-- default values-->
    <param name="disease_clinvarMIN" value="4" type="integer"/> 
    <param name="disease_clinvarMAX" value="6" type="integer"/> 
    <param name="score_AFMIN" value="2" type="integer"/> 
    <param name="score_AFMAX" value="4" type="integer"/> 
    <param name="score_functionalMIN" value="4" type="integer"/> 
    <param name="score_functionalMAX" value="6" type="integer"/> 
    <param name="score_NSMIN" value="2" type="integer"/> 
    <param name="score_NSMAX" value="4" type="integer"/> 
    <param name="score_nINDMIN" value="2" type="integer"/> 
    <param name="score_nINDMAX" value="4" type="integer"/> 
    <param name="AF" value="0.0001" type="float"/> 
    <param name="scoreeQTLMIN" value="2" type="integer"/> 
    <param name="scoreeQTLMAX" value="4" type="integer"/> 
    <param name="nind" value="5" min="5" type="integer"/> 
    <param name="scoreGMIN" value="3" type="integer"/> 
    <param name="scoreGMAX" value="5" type="integer"/> 
<!--optional values -->
    <param format="txt" name="kfile" type="data" optional="true" label="txt kfile" help="input kfile"/>
    <param format="txt" name="efile" type="data" optional="true" label="txt efile" help="input efile"/>
    <param format="txt" name="qfile" type="data" optional="true" label="txt qfile" help="input qfile"/>
    <param name="disease" type="text" optional="true"/>
    <param name="similarD" type="data" format="txt" optional="true"/>
    <param name="lgenes" type="data" format="txt" optional="true"/>
<!--others-->

  </inputs>
  <outputs>
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
    <data format="tabular" name="ofile" label="${tool.name} on ${on_string}: tabular "/>
  </outputs>
  <stdio>
  </stdio>
  <tests>
      <test>
      </test>
  </tests>
  <help>
**What it does**



**Important Usage Note**



  </help>
  <citations>
  </citations>
</tool>