diff --git a/tools/rgenetics/rgFastQC.xml b/tools/rgenetics/rgFastQC.xml
index 588a71e6c47..de36f2cb8ab 100644
--- a/tools/rgenetics/rgFastQC.xml
+++ b/tools/rgenetics/rgFastQC.xml
@@ -1,7 +1,7 @@
 <tool name="Fastqc: Fastqc QC" id="fastqc" version="0.5">
   <description>using FastQC from Babraham</description>
   <command interpreter="python">
-    rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -j $input_file.name -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc
+    rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc"
 #if $contaminants.dataset and str($contaminants) > ''
 -c "$contaminants"
 #end if