Bio-MUST-Core
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bin/export-itol.pl view on Meta::CPAN
# TODO: use standard BMC error message scheme
sub message {
my $response = shift;
my $outfile = shift;
if ( $response->is_success() ) {
my @res = split /\n/xms, $response->content;
# check for export error
if ($response->header('Content-type') =~ /text\/html/xms) {
warn <<"EOT";
Warning: export failed. iTOL returned the following error message:
$res[0]
EOT
}
# if no warnings, export tree to outfile
else {
### Exporting tree to: $outfile
open my $out, '>', $outfile;
say {$out} join "\n", @res;
}
}
else {
warn <<"EOT";
Warning: iTOL returned a web server error; full message follows:
EOT
print $response->as_string;
}
return;
}
__END__
=pod
=head1 NAME
export-itol.pl - Download formatted trees from iTOL
=head1 VERSION
version 0.252040
=head1 USAGE
export-itol.pl <infiles> [optional arguments]
=head1 REQUIRED ARGUMENTS
This script is based on C<iTOL_downloader.pl>.
=over
=item <infiles>
Path to input TSV tree id files [repeatable argument].
Such files are generated when uploading trees with the script L<import-itol.pl>.
=for Euclid: infiles.type: readable
repeatable
=back
=head1 OPTIONS
=over
=item --config=<file>
Path to input INI config file. When not specified, INI config files must have
the same basename as C<infiles> (but see C<--in-strip> below) [default: none].
A config file requires at least the C<format> argument. Supported outfile
formats are: C<svg>, C<pdf>, C<eps>, C<ps>, C<png>, C<newick>, C<nexus> and
C<phyloxml>.
To display all optional parameters and values, see iTOL help page:
L<https://itol.embl.de/help.cgi#bExOpt>
An example of INI config file follows:
format=svg
dpi=300
display_mode=2
current_font_name=Courier
datasets_visible=3
range_mode=2
include_ranges_legend=1
=for Euclid: file.type: readable
=item --in[-strip]=<str>
Substring(s) to strip from infile basenames before attempting to derive INI
infiles [default: none].
=for Euclid: str.type: string
repeatable
=item --out[-suffix]=<suffix>
Suffix to append to tree file basenames for deriving outfile names [default:
none].
=for Euclid: suffix.type: string
=item --version
=item --usage
=item --help
=item --man
Print the usual program information
=back
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