# HG changeset patch
# User davidvanzessen
# Date 1435060349 14400
# Node ID 1b356cbde3611b798041f68d822885497362acee
# Parent  b8db36cfe6ad05f3d239d666d9dc8e6f3f8f0b3e
Uploaded

diff -r b8db36cfe6ad -r 1b356cbde361 complete.sh
--- a/complete.sh	Mon Jan 12 11:07:58 2015 -0500
+++ b/complete.sh	Tue Jun 23 07:52:29 2015 -0400
@@ -53,9 +53,10 @@
 	parsedFileName="$PWD/$parsedFileName.parsed"
 	f=$(file $current)
 	zipType="Zip archive"
-  if [[ "$f" == *"$zipType"* ]]
+	zxType="XZ compressed data"
+  if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
 	then
-		echo "<tr><td>Sample $count of patient $id is a zip file, using IMGT Loader</td></tr>" >> $html
+		echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html
 	  fileName=$(basename $current)
 		imgtConvert $current $id $count $parsedFileName "${id}_${count}" #&
 	else
@@ -80,5 +81,5 @@
 
 echo "after ED"
 
-$dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $filterproductive
+$dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" $locus $filterproductive