| line |
true |
false |
branch |
|
105
|
0 |
1 |
if defined $cmd_version
|
|
106
|
0 |
1 |
if ($self->version)
|
|
117
|
0 |
1 |
if defined $help
|
|
118
|
0 |
1 |
if ($self->help)
|
|
124
|
0 |
1 |
if ($check_dependancies)
|
|
130
|
0 |
1 |
if (defined $verbose)
|
|
135
|
0 |
1 |
if (@{$self->args;} < 2)
|
|
139
|
0 |
1 |
if defined $output_filename
|
|
140
|
1 |
0 |
if defined $job_runner
|
|
141
|
0 |
1 |
if defined $makeblastdb_exec
|
|
142
|
0 |
1 |
if defined $blastp_exec
|
|
143
|
0 |
1 |
if defined $mcxdeblast_exec
|
|
144
|
0 |
1 |
if defined $mcl_exec
|
|
145
|
0 |
1 |
if defined $cpus
|
|
146
|
0 |
1 |
if defined $inflation_value
|
|
148
|
0 |
1 |
if (defined $perc_identity)
|
|
150
|
0 |
0 |
if ($perc_identity < 50)
|
|
157
|
0 |
1 |
if defined $mafft
|
|
158
|
0 |
1 |
if defined $apply_unknowns_filter
|
|
161
|
0 |
1 |
if (defined $output_multifasta_files)
|
|
162
|
0 |
0 |
if (which('prank')) { }
|
|
167
|
0 |
0 |
if (which('mafft')) { }
|
|
177
|
0 |
1 |
if defined $dont_delete_files
|
|
178
|
1 |
0 |
if defined $dont_split_groups
|
|
179
|
0 |
1 |
if defined $create_rplots
|
|
180
|
0 |
1 |
if defined $verbose_stats
|
|
181
|
1 |
0 |
if defined $translation_table
|
|
182
|
0 |
1 |
if defined $group_limit
|
|
183
|
0 |
1 |
if defined $kraken_db
|
|
184
|
0 |
1 |
if defined $output_directory
|
|
186
|
0 |
1 |
if (defined $verbose_stats and defined $output_multifasta_files)
|
|
191
|
0 |
1 |
if (defined $run_qc)
|
|
192
|
0 |
0 |
if (which('kraken') and which('kraken-report')) { }
|
|
200
|
0 |
1 |
if ($self->cpus > 1)
|
|
204
|
0 |
1 |
if defined $core_definition
|
|
207
|
0 |
3 |
unless (-e $filename)
|
|
214
|
0 |
1 |
if $self->dont_delete_files
|
|
219
|
1 |
0 |
if $self->output_directory eq '.' or $self->output_directory eq ''
|
|
221
|
0 |
0 |
if (-e $self->output_directory or -d $self->output_directory)
|
|
224
|
0 |
0 |
if (-e $self->output_directory or -d $self->output_directory)
|
|
229
|
0 |
0 |
if (@$err)
|
|
245
|
0 |
1 |
if $self->version or $self->help
|
|
252
|
0 |
1 |
if (@{$reformat_input_files->fixed_gff_files;} == 0)
|
|
271
|
0 |
1 |
if ($self->run_qc)
|
|
312
|
0 |
0 |
if (defined $Bio::Roary::CommandLine::Roary::VERSION) { }
|