# HG changeset patch
# User davidvanzessen
# Date 1435071245 14400
# Node ID 8dba36531e6eb786c839be5b15fa2f5bb2a9214c
# Parent  d436daae9d68517de3a9ab97e10e85c804b1ef1b
Uploaded

diff -r d436daae9d68 -r 8dba36531e6e wrapper.sh
--- a/wrapper.sh	Thu Jun 18 03:10:11 2015 -0400
+++ b/wrapper.sh	Tue Jun 23 10:54:05 2015 -0400
@@ -11,7 +11,18 @@
 unique=$8
 mkdir $outdir
 
-unzip $input -d $PWD/files/ > $PWD/unziplog.log
+type="`file $input`"
+if [[ "$type" == *"Zip archive"* ]] ; then
+	echo "Zip archive"
+	echo "unzip $input -d $PWD/files/"
+	unzip $input -d $PWD/files/
+elif [[ "$type" == *"XZ compressed data"* ]] ; then
+	echo "ZX archive"
+	echo "tar -xJf $input -C $PWD/files/"
+	mkdir -p $PWD/files/$title
+	tar -xJf $input -C $PWD/files/$title
+fi
+
 cat $PWD/files/*/1_* > $PWD/summary.txt
 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt