--- a/tassel.xml	Mon Jan 22 13:31:02 2024 +0000
+++ b/tassel.xml	Mon Jan 22 13:31:24 2024 +0000
@@ -7,44 +7,23 @@
         <!-- [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>$__tool_directory__/tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
-#if $analysis_opts.fonction_selector == "mlm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
- #end if
- -fork4 -k $analysis_opts.kinship
- -combineA -input1 -input2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -input3
- #end if
- -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 
- #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
-  -runfork3
- #end if
- -runfork4
- 
+    <command>
+#if $analysis_opts.fonction_selector == "ck":
+ mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
+#else if $analysis_opts.fonction_selector == "ld":
+ mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
 #else if $analysis_opts.fonction_selector == "glm":
- -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
- -fork2 -r $analysis_opts.trait
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
- #end if
- -combineA -input1 -input2 
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -input3
+ #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;
+ #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;
  #end if
- -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
- #if $analysis_opts.add_file.additional_file_selector == "yes":
-  -runfork3
- #end if 
-#else if $analysis_opts.fonction_selector == "ld":
- -fork1 -h $hapmap
- -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
-#else if $analysis_opts.fonction_selector == "ck":
- -fork1 -h $hapmap
- -ck -export tmpdir$$/kinship -runfork1
+#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$$/output6.txt $output3;
+ #else if $analysis_opts.add_structure_file.additional_file_selector == "yes":
+  mkdir tmpdir$$;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;
+ #end if
 #end if
 	</command>
 	<inputs>
@@ -116,7 +95,6 @@
 		
 		<data format="txt" name="log" label="Log file"/>
 	</outputs>
-​
     <tests>
         <test>
             <param name="hapmap" value="input_hapmap.txt"/>