Mercurial > repos > dereeper > roary_plots
comparison Roary/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t @ 0:c47a5f61bc9f draft
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author | dereeper |
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date | Fri, 14 May 2021 20:27:06 +0000 |
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-1:000000000000 | 0:c47a5f61bc9f |
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1 #!/usr/bin/env perl | |
2 use Moose; | |
3 use Data::Dumper; | |
4 use Cwd; | |
5 use File::Which; | |
6 | |
7 BEGIN { unshift( @INC, './lib' ) } | |
8 BEGIN { unshift( @INC, './t/lib' ) } | |
9 with 'TestHelper'; | |
10 | |
11 BEGIN { | |
12 use Test::Most; | |
13 use_ok('Bio::Roary::CommandLine::GeneAlignmentFromNucleotides'); | |
14 } | |
15 | |
16 my $script_name = 'Bio::Roary::CommandLine::GeneAlignmentFromNucleotides'; | |
17 my $cwd = getcwd(); | |
18 system('touch empty_file'); | |
19 system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa'); | |
20 my %scripts_and_expected_files = ( | |
21 't/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta.fa.aln' ], | |
22 '-h' => [ 'empty_file', 't/data/empty_file' ], | |
23 ); | |
24 | |
25 SKIP: | |
26 { | |
27 skip "prank not installed", 2 unless ( which('prank') ); | |
28 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files ); | |
29 } | |
30 | |
31 SKIP: | |
32 { | |
33 skip "mafft not installed", 2 unless ( which('mafft') ); | |
34 system('cp t/data/nuc_to_be_aligned.fa t/data/f.fa'); | |
35 %scripts_and_expected_files = ( | |
36 '--mafft t/data/f.fa' => [ 't/data/f.fa.aln', 't/data/expected_nuc_multifasta_mafft.fa.aln' ], | |
37 ); | |
38 mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files ); | |
39 } | |
40 | |
41 done_testing(); |