diff --git a/tools/filters/gff/gtf_filter_by_attribute_values_list.py b/tools/filters/gff/gtf_filter_by_attribute_values_list.py
index f1754f1bf3a..8be10348557 100644
--- a/tools/filters/gff/gtf_filter_by_attribute_values_list.py
+++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.py
@@ -53,13 +53,15 @@ def gff_filter(gff_file, attribute_name, ids_file, output_file):
         ids_dict[line.split('\t')[0].strip()] = True
 
     # Filter GFF file using ids.
-    output = open(output_file, 'w')
-    for line in open(gff_file):
-        fields = line.split('\t')
-        attributes = parse_gff_attributes(fields[8])
-        if (attribute_name in attributes) and (attributes[attribute_name] in ids_dict):
-            output.write(line)
-    output.close()
+    with open(output_file, 'w') as output, open(gff_file) as ingff:
+        for line in ingff:
+            if not line or line.startswith('#'):
+                output.write(line)
+                continue
+            fields = line.split('\t')
+            attributes = parse_gff_attributes(fields[8])
+            if attribute_name in attributes and attributes[attribute_name] in ids_dict:
+                output.write(line)
 
 
 if __name__ == "__main__":
diff --git a/tools/filters/gff/gtf_filter_by_attribute_values_list.xml b/tools/filters/gff/gtf_filter_by_attribute_values_list.xml
index 0f5d0dadabc..b1063b78827 100644
--- a/tools/filters/gff/gtf_filter_by_attribute_values_list.xml
+++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.xml
@@ -1,8 +1,11 @@
-<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">
+<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.2">
     <description></description>
-    <command interpreter="python">
-      gtf_filter_by_attribute_values_list.py $input $attribute_name $ids $output
-    </command>
+    <requirements>
+        <requirement type="package" version="3.6">python</requirement>
+    </requirements>
+    <command><![CDATA[
+python '$__tool_directory__/gtf_filter_by_attribute_values_list.py' '$input' $attribute_name '$ids' '$output'
+    ]]></command>
     <inputs>
         <param format="gtf" name="input" type="data" label="Filter"/>
         <param name="attribute_name" type="select" label="Using attribute name">
@@ -19,10 +22,10 @@
     <tests>
         <!-- Test filtering with a simple list of values. -->
         <test>
-            <param name="input" value="gops_subtract_in1.gff"/>
+            <param name="input" value="gops_subtract_in1_wcomment.gff"/>
             <param name="attribute_name" value="gene_id"/>
             <param name="ids" value="gtf_filter_by_attribute_values_list_in1.txt"/>
-            <output name="output" file="gtf_filter_by_attribute_values_list_out1.gtf"/>
+            <output name="output" file="gtf_filter_by_attribute_values_list_out1_wcomment.gtf"/>
         </test>
         <!-- Test filtering with a more complex tabular file. -->
         <test>