--- a/old_version/optimizer.xml	Wed Jul 22 19:20:30 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-<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>