--- a/tassel.xml	Mon Jan 22 13:31:24 2024 +0000
+++ b/tassel.xml	Tue Oct 22 09:23:33 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="Tassel" name="Tassel" version="2.0.0">
+<tool id="Tassel" name="Tassel" version="3.0.0">
 	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
 	<requirements>
 				<requirement type="package" version="5.2.89">tassel</requirement>
@@ -9,25 +9,25 @@
     </stdio>
     <command>
 #if $analysis_opts.fonction_selector == "ck":
- mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
+ mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
 #else if $analysis_opts.fonction_selector == "ld":
- mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
+ mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
 #else if $analysis_opts.fonction_selector == "glm":
  #if $analysis_opts.add_file.additional_file_selector == "no":
-  mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
+  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
  #else if $analysis_opts.add_file.additional_file_selector == "yes":
-  mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
+  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
  #end if
 #else if $analysis_opts.fonction_selector == "mlm":
  #if $analysis_opts.add_structure_file.additional_file_selector == "no": 
-  mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3;
+  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
  #else if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3;
+  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
  #end if
 #end if
 	</command>
 	<inputs>
-		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
+		<param format="vcf" name="vcffile" type="data" label="VCF file"/>
 		<conditional name="analysis_opts">
 			<param name="fonction_selector" type="select" label="Type of analysis">
 				<option value="mlm" selected="True">MLM</option>
@@ -97,18 +97,18 @@
 	</outputs>
     <tests>
         <test>
-            <param name="hapmap" value="input_hapmap.txt"/>
+            <param name="vcffile" value="input.vcf"/>
             <conditional name="analysis_opts">
                 <param name="fonction_selector" value="glm"/>
-                <param name="trait" value="phenotyping_DRB.csv"/>
+                <param name="trait" value="phenotyping_xantho.tsv"/>
                 <conditional name="add_structure_file">
                     <param name="additional_file_selector" value="yes"/>
-                    <param name="structure" value="Best_K_Output"/>
+                    <param name="structure" value="Best_K_Output2"/>
                 </conditional>
             </conditional>
             <param name="filterAlignMinFreq" value="0.05"/>
-            <output name="output1" value="Tassel_output.txt"/>
-            <output name="output2" value="Allele_effects.txt"/>
+            <output name="output1" value="statistics_output.txt"/>
+            <output name="output2" value="Allele_effects_output.txt"/>
         </test>
     </tests>
     <help><![CDATA[