# HG changeset patch
# User davidvanzessen
# Date 1481899989 18000
# Node ID 96c1276ceefee0a5248ee192381adb747727bd3e
# Parent  22fabe161cf38d703207be0c4ed6ceb59bd6df0d
Uploaded

diff -r 22fabe161cf3 -r 96c1276ceefe shm_csr.xml
--- a/shm_csr.xml	Thu Dec 15 09:44:17 2016 -0500
+++ b/shm_csr.xml	Fri Dec 16 09:53:09 2016 -0500
@@ -1,7 +1,7 @@
 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
+		wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
diff -r 22fabe161cf3 -r 96c1276ceefe wrapper.sh
--- a/wrapper.sh	Thu Dec 15 09:44:17 2016 -0500
+++ b/wrapper.sh	Fri Dec 16 09:53:09 2016 -0500
@@ -6,7 +6,7 @@
 log=$3 #becomes the main html page at the end
 outdir=$4
 output="$outdir/index.html" #copied to $log location at the end
-title=$5
+title="$5"
 include_fr1=$6
 functionality=$7
 unique=$8
@@ -37,8 +37,8 @@
 elif [[ "$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
+	mkdir -p "$PWD/files/$title"
+	tar -xJf $input -C "$PWD/files/$title"
 fi
 
 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
@@ -439,7 +439,7 @@
 	mkdir $outdir/baseline/IGG
 	if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
 		cd $outdir/baseline/IGG
-		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
+		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
 	else
 		echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
 	fi