--- a/tassel.xml	Fri Aug 24 08:33:49 2018 -0400
+++ b/tassel.xml	Mon Dec 11 15:12:25 2023 +0000
@@ -2,14 +2,15 @@
 	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
 	<requirements>
                 <requirement type="package" version="5.2.40">tassel</requirement>
+				<requirement type="package" version="1.8">openjdk</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$$/
+​
+	<command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
 #if $analysis_opts.fonction_selector == "mlm":
  -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
  -fork2 -r $analysis_opts.trait
@@ -48,7 +49,7 @@
  -fork1 -h $hapmap
  -ck -export tmpdir$$/kinship -runfork1
 #end if
-	</command>
+	]]></command>
 	<inputs>
 		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
 		<conditional name="analysis_opts">
@@ -118,7 +119,7 @@
 		
 		<data format="txt" name="log" label="Log file"/>
 	</outputs>
-
+​
     <tests>
         <test>
             <param name="hapmap" value="input_hapmap.txt"/>
@@ -135,47 +136,47 @@
             <output name="output2" value="Allele_effects.txt"/>
         </test>
     </tests>
-
+​
     <help><![CDATA[
-
-
+​
+​
 .. class:: infomark
-
+​
 **Tassel5** version 5.2.40
-
+​
 .. class:: infomark
-
+​
 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
-
+​
 .. class:: infomark
-
+​
 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
-
+​
 ---------------------------------------------------
-
+​
 =======
 Tassel5
 =======
-
+​
 -----------
 Description
 -----------
-
+​
   | 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/
-
+​
 ------------
 Dependencies
 ------------
 Tassel5
         tassel_ 5.2.40, Conda version
-
+​
 .. _tassel: https://anaconda.org/bioconda/tassel
-
+​
     ]]></help>
     <citations>
        <citation type="doi">10.1093/bioinformatics/btm308</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file