--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tassel/tassel.sh	Thu Feb 26 01:15:36 2015 -0500
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+analyseType=$1;
+out1=$2;
+out2=$3;
+out3=$4;
+log1=$5;
+galaxyOutDir=$6;
+
+
+mkdir $galaxyOutDir
+
+# Suppression des 6 premiers arguments de la liste des arguments $@
+shift; shift; shift; shift; shift; shift;
+
+if [[ $analyseType == glm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELGLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELGLM2.txt" $out2
+fi
+
+if [[ $analyseType == mlm ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/TASSELMLM1.txt" $out1
+ mv "$galaxyOutDir/TASSELMLM2.txt" $out2
+ mv "$galaxyOutDir/TASSELMLM3.txt" $out3
+fi
+
+if [[ $analyseType == ld ]] 
+then
+ run_pipeline.pl $* >> $log1 2>&1
+fi
+
+
+if [[ $analyseType == ck ]]
+then
+ run_pipeline.pl $* >> $log1 2>&1
+ mv "$galaxyOutDir/kinship.txt" $out1
+fi