diff Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t @ 0:c47a5f61bc9f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t	Fri May 14 20:27:06 2021 +0000
@@ -0,0 +1,41 @@
+#!/usr/bin/env perl
+use Moose;
+use Data::Dumper;
+use Cwd;
+use File::Which;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, './t/lib' ) }
+with 'TestHelper';
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::Roary::CommandLine::GeneAlignmentFromNucleotides');
+}
+
+my $script_name = 'Bio::Roary::CommandLine::GeneAlignmentFromNucleotides';
+my $cwd         = getcwd();
+system('touch empty_file');
+system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa');
+my %scripts_and_expected_files = (
+    't/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta.fa.aln' ],
+    '-h'          => [ 'empty_file',      't/data/empty_file' ],
+);
+
+SKIP:
+{
+    skip "prank not installed", 2 unless ( which('prank') );
+    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
+}
+
+SKIP:
+{
+    skip "mafft not installed", 2 unless ( which('mafft') );
+	system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa');
+	%scripts_and_expected_files = (
+	    '--mafft t/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta_mafft.fa.aln' ],
+	);
+    mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
+}
+
+done_testing();