--- a/wrapper.sh	Wed Jun 29 05:13:25 2016 -0400
+++ b/wrapper.sh	Wed Jul 13 08:04:13 2016 -0400
@@ -148,22 +148,9 @@
 echo "---------------- aa_histogram.r ----------------"
 echo "---------------- aa_histogram.r ----------------<br />" >> $log
 
-Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png "" 2>&1
-
-echo "---------------- aa_histogram.r ca ----------------"
-echo "---------------- aa_histogram.r ca ----------------<br />" >> $log
-
-Rscript $dir/aa_histogram.r $outdir/aa_mutations_ca.txt $outdir/aa_histogram_ca.png "ca" 2>&1
-
-echo "---------------- aa_histogram.r cg ----------------"
-echo "---------------- aa_histogram.r cg ----------------<br />" >> $log
-
-Rscript $dir/aa_histogram.r $outdir/aa_mutations_cg.txt $outdir/aa_histogram_cg.png "cg" 2>&1
-
-echo "---------------- aa_histogram.r cm ----------------"
-echo "---------------- aa_histogram.r cm ----------------<br />" >> $log
-
-Rscript $dir/aa_histogram.r $outdir/aa_mutations_cm.txt $outdir/aa_histogram_cm.png "cm" 2>&1
+cp $outdir/aa_mutations.txt $outdir/aa_mutations_count.txt
+Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1
+mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
 
 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
 
@@ -384,5 +371,5 @@
 cp $outdir/index.html $log
 
 echo "---------------- Done! ----------------"
-echo "---------------- Done! ----------------<br />" >> $log
+echo "---------------- Done! ----------------<br />" >> $outdir/log.html