--- a/complete.sh	Mon Sep 08 04:24:04 2014 -0400
+++ b/complete.sh	Mon Jan 05 09:30:08 2015 -0500
@@ -6,7 +6,7 @@
 clonalType=$4
 species=$5
 locus=$6
-selection=$7
+filterproductive=$7
 
 html=$2
 dir="$(cd "$(dirname "$0")" && pwd)"
@@ -23,7 +23,6 @@
 	echo "igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
 	/home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4
 	echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
-
 	echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
 	perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > "$5"
 	echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
@@ -33,7 +32,6 @@
 	echo "<tr><td>Starting imgt convert of sample $3 of patient $2</td></tr>" >> $html
 	bash $dir/imgt_loader.sh $1 $4 $5
 	echo "<tr><td>Finished conversion of sample $3 of patient $2</td></tr>" >> $html
-	
 }
 
 id=""
@@ -82,17 +80,5 @@
 
 echo "after ED"
 
-if [ "$locus" == "igh" ] || [ "$locus" == "igk" ] || [ "$locus" == "igl" ]; then
-	bash $dir/r_wrapper_b.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection
-else
-	bash $dir/r_wrapper_t.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $selection
-fi
-
+$dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $filterproductive
 
-
-
-
-
-
-
-