--- a/tassel.xml	Thu Nov 02 05:19:30 2017 -0400
+++ b/tassel.xml	Mon Apr 16 08:54:41 2018 -0400
@@ -1,8 +1,14 @@
-<tool id="Tassel" name="Tassel" version="5.0">
-	<description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
+<tool id="Tassel" name="Tassel" version="2.0.0">
+	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
 	<requirements>
-                <requirement type="package" version="5.0">tassel</requirement>
+                <requirement type="package" version="5.2.40">tassel</requirement>
         </requirements>
+
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
 	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
 #if $analysis_opts.fonction_selector == "mlm":
  -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
@@ -62,6 +68,8 @@
 					<when value="yes">
 						<param format="txt" name="structure" type="data" label="Structure file"/>
 					</when>
+                                        <when value="no">
+                                        </when>
 				</conditional>
 			</when>
 			<when value="mlm">
@@ -75,6 +83,8 @@
 					<when value="yes">
 						<param format="txt" name="structure" type="data" label="Structure file"/>
 					</when>
+                                        <when value="no">
+                                        </when>
 				</conditional>
 				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
 					<option value="P3D" selected="True">P3D</option>
@@ -108,46 +118,64 @@
 		
 		<data format="txt" name="log" label="Log file"/>
 	</outputs>
-	<help>
+
+    <tests>
+        <test>
+            <param name="hapmap" value="input_hapmap.txt"/>
+            <conditional name="analysis_opts">
+                <param name="fonction_selector" value="glm"/>
+                <param name="trait" value="phenotyping_DRB.csv"/>
+                <conditional name="add_structure_file">
+                    <param name="additional_file_selector" value="yes"/>
+                    <param name="structure" value="Best_K_Output"/>
+                </conditional>
+            </conditional>
+            <param name="filterAlignMinFreq" value="0.05"/>
+            <output name="output1" value="Tassel_output.txt"/>
+            <output name="output2" value="Allele_effects.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
 
 .. class:: infomark
 
-**Program encapsulated in Galaxy by Southgreen**
+**Tassel5** version 5.2.40
+
+.. class:: infomark
+
+**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
 
 .. class:: infomark
 
-**Tassel**
-
------
+**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
 
-==========
- Authors:
-==========
+---------------------------------------------------
 
-**Terry Casstevens**
-
------
+=======
+Tassel5
+=======
 
-==========
- Overview
-==========
+-----------
+Description
+-----------
 
-Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
+  | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
+  | For further informations on tassel, please visit the website_.
 
------
+.. _website: http://www.maizegenetics.net/tassel/
 
-For further informations, please visite the website of TASSEL_.
-
-
-.. _TASSEL: http://www.maizegenetics.net/tassel/
+------------
+Dependencies
+------------
+Tassel5
+        tassel_ 5.2.40, Conda version
 
-	</help>
-<!--
-<tests>
-  <test>
-      <param name="input" value="genotyping_file.inp" />
-      <output name="output" file="phase_output" />
-   </test>
-</tests>
--->
+.. _tassel: https://anaconda.org/bioconda/tassel
+
+    ]]></help>
+    <citations>
+       <citation type="doi">10.1093/bioinformatics/btm308</citation>
+    </citations>
 </tool>