--- a/wrapper.sh	Thu Apr 16 09:36:19 2015 -0400
+++ b/wrapper.sh	Thu Jun 18 03:10:11 2015 -0400
@@ -7,6 +7,8 @@
 outdir=$4
 title=$5
 include_fr1=$6
+functionality=$7
+unique=$8
 mkdir $outdir
 
 unzip $input -d $PWD/files/ > $PWD/unziplog.log
@@ -40,7 +42,7 @@
 
 
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"
@@ -74,7 +76,7 @@
 	fi
 done < $outdir/result.txt
 echo "</table>" >> $output
-echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br />" >> $output
+echo "<a href='unmatched.txt'>unmatched</a><br /><a href='motif_per_seq.txt'>motif per sequence</a><br /><a href='merged.txt'>all data</a><br />" >> $output
 
 
 echo "<img src='all.png'/><br />" >> $output