--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/Output/QueryGroups.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,73 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Data::Dumper;
+use Moose;
+BEGIN { unshift( @INC, './t/lib' ) }
+with 'TestHelper';
+
+BEGIN { unshift( @INC, './lib' ) }
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::Output::QueryGroups');
+}
+
+my $plot_groups_obj = Bio::Roary::AnalyseGroups->new(
+    fasta_files     => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
+    groups_filename => 't/data/query_groups'
+);
+
+my $obj;
+ok($obj = Bio::Roary::Output::QueryGroups->new(
+    analyse_groups  => $plot_groups_obj,
+    input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
+  ),'initialise groups query object');
+  
+ok($obj->groups_union(), 'create the union file');
+ok($obj->groups_intersection(), 'create the intersection file');
+ok($obj->groups_complement(), 'create the complement file');
+
+compare_files('union_of_groups.gg','t/data/expected_union_of_groups.gg', 'contents of the union groups as expected');
+compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups.gg', 'contents of the intersection groups as expected');
+compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups.gg', 'contents of the complement groups as expected');
+
+######################################
+# test varying core definition
+ok($obj = Bio::Roary::Output::QueryGroups->new(
+    analyse_groups  => $plot_groups_obj,
+    input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
+    core_definition => 0.66
+  ),'initialise groups query object');
+  
+ok($obj->groups_intersection(), 'create the intersection file');
+ok($obj->groups_complement(), 'create the complement file');
+
+compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_core0.66.gg', 'contents of the intersection groups as expected');
+compare_files('complement_of_groups.gg', 't/data/expected_complement_of_groups_core0.66.gg', 'contents of the complement groups as expected');
+
+
+unlink('union_of_groups.gg');
+unlink('intersection_of_groups.gg');
+unlink('complement_of_groups.gg');
+
+######################################
+
+$plot_groups_obj = Bio::Roary::AnalyseGroups->new(
+    fasta_files     => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ],
+    groups_filename => 't/data/query_groups_paralogs'
+);
+
+ok($obj = Bio::Roary::Output::QueryGroups->new(
+    analyse_groups  => $plot_groups_obj,
+    input_filenames => [ 't/data/query_1.fa', 't/data/query_2.fa','t/data/query_3.fa' ]
+  ),'initialise groups query object with paralogs');
+  
+ok($obj->groups_intersection(), 'create the intersection file');
+
+compare_files('intersection_of_groups.gg', 't/data/expected_intersection_of_groups_paralogs.gg', 'contents of the intersection groups with paralogs as expected');
+unlink('intersection_of_groups.gg');
+
+
+done_testing();
+