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Fix usage text #122

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merged 2 commits into from
May 16, 2015
Merged

Fix usage text #122

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f4fe3b2
usage text prints out when no parameters passed in
andrewjpage May 14, 2015
abfe082
update version
andrewjpage May 14, 2015
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2 changes: 1 addition & 1 deletion dist.ini
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
name = Bio-Roary
version = 2.2.0
version = 2.2.1
author = Andrew J. Page <ap13@sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
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8 changes: 2 additions & 6 deletions lib/Bio/Roary/CommandLine/Roary.pm
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Expand Up @@ -41,7 +41,6 @@ has 'group_limit' => ( is => 'rw', isa => 'Num', default => 50000 );
has 'core_definition' => ( is => 'rw', isa => 'Num', default => 1 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );

has '_error_message' => ( is => 'rw', isa => 'Str' );
has 'run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );

sub BUILD {
Expand Down Expand Up @@ -93,6 +92,7 @@ sub BUILD {
if(@{$self->args} == 0)
{
$self->logger->error("Error: You need to provide a GFF file");
die $self->usage_text;
}
$self->output_filename($output_filename) if ( defined($output_filename) );
$self->job_runner($job_runner) if ( defined($job_runner) );
Expand Down Expand Up @@ -139,7 +139,7 @@ sub BUILD {
for my $filename ( @{ $self->args } ) {
if ( !-e $filename ) {
$self->logger->error("Error: Cant access file $filename");
last;
die $self->usage_text;
}
}
$self->fasta_files( $self->args );
Expand All @@ -150,10 +150,6 @@ sub run {
my ($self) = @_;

( !$self->help ) or die $self->usage_text;
if ( defined( $self->_error_message ) ) {
print $self->_error_message . "\n";
die $self->usage_text;
}

$self->logger->info("Extracting proteins from GFF files");
my $prepare_input_files = Bio::Roary::PrepareInputFiles->new(
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