--- a/wrapper.sh	Thu Apr 02 03:31:23 2015 -0400
+++ b/wrapper.sh	Tue Apr 07 03:52:34 2015 -0400
@@ -6,6 +6,7 @@
 output=$3
 outdir=$4
 title=$5
+include_fr1=$6
 mkdir $outdir
 
 unzip $input -d $PWD/files/ > $PWD/unziplog.log
@@ -14,7 +15,7 @@
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
 
-#BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
+BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
 
 echo "${BLASTN_DIR}"
 
@@ -46,7 +47,7 @@
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"
-Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir 2>&1
+Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
 echo "python mutation analysis"
 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt
 
@@ -82,6 +83,10 @@
 then
 	echo "<img src='cg.png'/><br />" >> $output
 fi
+if [ -a $outdir/scatter.png ]
+then
+	echo "<img src='scatter.png'/><br />" >> $output
+fi
 
 for gene in ${genes[@]}
 do