From e4d9e1a29e898af13fcf66e7a4b809d10016bd8e Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 13 Feb 2021 20:38:05 +0100
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 tools/filters/gff/gtf_filter_by_attribute_values_list.py  | 3 +--
 tools/filters/gff/gtf_filter_by_attribute_values_list.xml | 6 +++---
 2 files changed, 4 insertions(+), 5 deletions(-)

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 cb641f40e05..8be10348557 100644
--- a/tools/filters/gff/gtf_filter_by_attribute_values_list.py
+++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.py
@@ -60,9 +60,8 @@ def gff_filter(gff_file, attribute_name, ids_file, output_file):
                 continue
             fields = line.split('\t')
             attributes = parse_gff_attributes(fields[8])
-            if (attribute_name in attributes) and (attributes[attribute_name] in ids_dict):
+            if attribute_name in attributes and attributes[attribute_name] in ids_dict:
                 output.write(line)
-        output.close()
 
 
 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 9dee10a0dca..c75b12d65a2 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 +1,8 @@
 <tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">
     <description></description>
-    <command>
-        python '$__tool_directory__/gtf_filter_by_attribute_values_list.py' '$input' '$attribute_name' '$ids' '$output'
-    </command>
+    <command><![CDATA[
+python '$__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">