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