--- a/galaxy/wrappers/VolcanoPlotTool.xml	Fri Jun 26 09:45:41 2020 -0400
+++ b/galaxy/wrappers/VolcanoPlotTool.xml	Wed Sep 09 10:38:06 2020 +0000
@@ -1,4 +1,4 @@
-<tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.3">
+<tool name="GIANT-Plot volcanos" id="giant_volcano_plot" version="0.3.4">
   <description>Plot volcano from tabular file</description>
   <requirements>
     <requirement type="package" version="1.7.1">r-r.methodss3</requirement>
@@ -8,6 +8,7 @@
     <requirement type="package" version="1.3.1">r-stringr</requirement>
   </requirements>
   <code file="../../src/General_functions.py"/>
+  <!--<code file="./src/General_functions.py"/> change for Planemo test-->
   <stdio>
     <regex match="Execution halted"
            source="both"
@@ -25,6 +26,8 @@
     #import imp
     #set $runIdentifier=str($outputData).rsplit("/")[-1].rsplit(".")[0]
     #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py')
+    ##change for Planemo test
+    ##set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/src/General_functions.py')
     #set $ret_code=$general_functions.selectSubSetTable($inputSection['inputData'].file_name,$inputSection['headerNumber'].value,[0],$volcanoSection['volcanoList'],$__new_file_path__+'/'+$__user_id__+'_'+$runIdentifier+'_statisticsFormated.csv',$log.file_name)
 
     if [ $ret_code != 0 ]; then
@@ -44,6 +47,8 @@
 
 
     Rscript '$__tool_directory__/../../src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf'
+    ##change for Planemo test
+    ##Rscript '$__tool_directory__/src/VolcanoPlotsScript.R' -i 'statisticsFormated.csv' -l '$log' -o '$outputData' -f 'pdf'
       #for $i, $s in enumerate( $volcanoSection.volcanoList )
         -n '${s.volcanoName}'
         -p '${s.pvalColumn}'
@@ -324,25 +329,44 @@
   </outputs>
 
 
-  
+
  <tests>
   <test maxseconds="3600">
-    <param name="wfile" value="wiggle.wig" />
-    <param name="bfile" value="bedfile.bed" />
-    <param name="span" value="3000" />
-    <param name="pfres" value="50" />
-    <param name="lowersize" value="1000" />
-    <param name="middlesize" value="2000" />
-    <param name="uppersize" value="3000" />
-    <param name="lowerbisize" value="2500" />
-    <param name="upperbisize" value="5000" />
-    <param name="reldist" value="3000" />
-    <param name="genome" value="hg18" />
-    <param name="imagetype" value="PDF" />
-    <param name="enable" value="no" />
-    <output name="outputData" file="ceas_1/ceas_1.pdf" />
+    <section name="inputSection">
+      <param name="inputData" value="./DiffExprLimma/output/outputStat.csv" />
+      <param name="headerNumber" value="2" />
+    </section>
+    <section name="volcanoSection" >
+      <repeat name="volcanoList" >
+        <param name="volcanoName" value="TreatVsControl" />
+        <param name="pvalColumn" value="TreatVsControl_p-val" />
+        <param name="fdrColumn" value="TreatVsControl_FDR.p-val" />
+        <param name="fcColumn" value="TreatVsControl_log2(FC)" />
+      </repeat>
+      <repeat name="volcanoList" >
+        <param name="volcanoName" value="WTvsKO" />
+        <param name="pvalColumn" value="WTvsKO_p-val" />
+        <param name="fdrColumn" value="WTvsKO_FDR.p-val" />
+        <param name="fcColumn" value="WTvsKO_log2(FC)" />
+      </repeat>
+    </section>
+    <section name="plotSection" >
+      <param name="fcKind" value="log2(FC)" />
+      <param name="FDRthreshold" value="0.05" />
+      <param name="FCthreshold" value="2.0" />
+      <conditional name="geneInformation">
+        <param name="addGeneInfo" value="false" />
+      </conditional>
+      <param type="select" value="png" />
+    </section>
+    <output name="outputData" file="./VolcanoPlotTool/output/outputResults.csv" />
+    <output name="html_file" file="./VolcanoPlotTool/output/outputHTML.zip" decompress="true" />
+    <output name="log" file="./VolcanoPlotTool/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
   </test>
-</tests> 
+ </tests> 
+
+
+
   <help>
 <![CDATA[
 **What it does ?**