Mercurial > repos > cpt > cpt_psm_plotter

annotate lib/CPT/GalaxyGetOpt.pm @ 1:8691c1c61a8e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 package CPT::GalaxyGetOpt;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2 use CPT::ParameterGroup;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 use autodie;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
4 use File::Spec::Functions qw[ catfile catdir ];
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
5 use Carp;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
6 no warnings;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 use Moose;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9 has 'appdesc' => ( is => 'rw', isa => 'Str', default => sub { 'No application description provided' } );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10 has 'appid' => ( is => 'rw', isa => 'Str', default => sub { "unknown_app_$0" } );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 has 'appname' => ( is => 'rw', isa => 'Str', default => sub { "Unnamed application $0"} );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12 has 'appvers' => ( is => 'rw', isa => 'Str', default => sub { '0.0.1' } );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 has 'registered_outputs' => ( is => 'rw', isa => 'HashRef' );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14 has 'opt' => ( is => 'rw', isa => 'Any');
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15 has filetype_detector => (
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16 is => 'rw',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 isa => 'Any',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21 sub getOptions {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 my ( $self, %passed_opts ) = @_;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 require Getopt::Long::Descriptive;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
24 # these get pushed through, thankfully. This way we can manually check for --genenrate_galaxy_export and exit slightly earlier.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 my %args = map { $_ => 1 } @ARGV;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 # Sections passed to us
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 my @script_args = @{ $passed_opts{'options'} };
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 my %defaults = @{ $passed_opts{'defaults'} };
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 # Output Files Stuff
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33 my @getopt_formatted_outputs;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34 my %outputs;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 # This is originally an array of output files. We transform to a hash for
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 # easier lookup
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 foreach(@{$passed_opts{'outputs'}}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 # Grab name/desc/opts
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 my ($name, $desc, $opts) = @{$_};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40 $outputs{$name} = {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41 description => $desc,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42 options => $opts,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 required => 1,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 };
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 my %tmp_opts_fix = %{$opts};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 $tmp_opts_fix{required} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47 $tmp_opts_fix{validate} = 'File/Output';
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48 push(@getopt_formatted_outputs, [$name, $desc, \%tmp_opts_fix]);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
49
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
50 # Adds the {name}_files_path special parameter
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
51 my %fp_opts = %{$opts};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
52 $fp_opts{hidden} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
53 $fp_opts{value} = "${name}.files_path";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
54 $fp_opts{default} = "${name}.files_path";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
55 $fp_opts{required} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
56 $fp_opts{_galaxy_specific} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
57 $fp_opts{validate} = "String";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
58 #$fp_opts{_show_in_galaxy} = 0;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
59 my $desc2 = "Associated HTML files for $name";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
60 my $name2 = "${name}_files_path";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
61 my @files_path = ($name2, $desc2, \%fp_opts);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
62 push(@getopt_formatted_outputs, \@files_path);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
63
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
64 # Adds the {name}_format special parameter
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
65 my %fp_opts3 = %{$opts};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
66 #$fp_opts3{hidden} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
67 $fp_opts3{default} = $fp_opts3{"default_format"};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
68 $fp_opts3{validate} = "File/OutputFormat";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
69 $fp_opts{required} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
70 #$fp_opts3{_galaxy_specific} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
71 #$fp_opts3{_show_in_galaxy} = 0;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
72 my $desc3 = "Associated Format for $name";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
73 my $name3 = "${name}_format";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
74 my @files_path3 = ($name3, $desc3, \%fp_opts3);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
75 push(@getopt_formatted_outputs, \@files_path3);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
76
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
77 # Adds the {name}_files_path special parameter
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
78 my %fp_opts4 = %{$opts};
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
79 $fp_opts4{hidden} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
80 $fp_opts4{value} = "${name}.id";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
81 $fp_opts4{default} = "${name}.id";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
82 $fp_opts4{validate} = "String";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
83 $fp_opts4{_galaxy_specific} = 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
84 #$fp_opts4{_show_in_galaxy} = 0;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
85 my $desc4 = "Associated ID Number for $name";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
86 my $name4 = "${name}_id";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
87 my @files_path4 = ($name4, $desc4, \%fp_opts4);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
88 push(@getopt_formatted_outputs, \@files_path4);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
89
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
90 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
91 $self->registered_outputs(\%outputs);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
92
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
93
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
94 # Store the application's name and description
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
95 if($defaults{appdesc}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
96 $self->appdesc($defaults{appdesc});
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
97 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
98 if($defaults{appid}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
99 $self->appid($defaults{appid});
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
100 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
101 if($defaults{appname}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
102 $self->appname($defaults{appname});
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
103 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
104 if($defaults{appvers}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
105 $self->appvers($defaults{appvers});
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
106 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
107
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
108 my $usage_desc;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
109 if ( $self->appname() && $self->appdesc() ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
110 $usage_desc = sprintf( "%s: %s\n%s [options] <some-arg>", $self->appname(), $self->appdesc(), $0 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
111 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
112
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
113 # Individual parameter parsers
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
114 require CPT::Parameter;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
115 # Which are stored in a collection of them
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
116 require CPT::ParameterCollection;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
117
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
118
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
119 my $parameterCollection = CPT::ParameterCollection->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
120
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
121 $parameterCollection->push_params(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
122 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
123 #['Standard Options'],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
124 #@extra_params,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
125 #[],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
126 ['outfile_supporting' , 'File or folder to output to, necessary when (class == Report || multiple calls to classyReturnResults || multiple standalone output files)' , { hidden => 1, validate => 'String', default => '__new_file_path__', _galaxy_specific => 1, _show_in_galaxy => 0 }],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
127 ['galaxy' , 'Run with galaxy-specific overrides' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
128 ['generate_galaxy_xml' , 'Generate a compatible galaxy-xml file. May need editing' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
129 [],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
130 ['Script Options'],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
131 ]
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
132 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
133
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
134 # If there's a default specified, we should apply that.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
135 foreach (@script_args) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
136 # If it's an array, push as is, because either it's old style/label/empty
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
137 # However, this doesn't allow setting defaults for things that aren't parameters
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
138 # and it won't set defaults for old style
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
139 if ( ref $_ eq 'ARRAY' ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
140 $parameterCollection->push_param($_);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
141 }elsif( ref $_ eq 'HASH'){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
142 my $pG = CPT::ParameterGroup->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
143 $pG->set_data($_);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
144 $parameterCollection->push_group($pG);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
145 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
146 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
147
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 # Our magic output files stuff
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 $parameterCollection->push_params(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151 [],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 ['Output Files'],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 @getopt_formatted_outputs,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154 ]
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157 # Other standard options like verbosity/version/etc
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158 $parameterCollection->push_params(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 [],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 ['Other Standard Options'],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 ['verbose|v', 'Be more verbose', {validate => 'Flag', _show_in_galaxy => 0}],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 ['version', 'Print version information', {validate => 'Flag', _show_in_galaxy => 0}],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 ['help', 'Print usage message and exit', {validate => 'Flag', _show_in_galaxy => 0}],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 # If we want the galaxy_xml, do that before the reduction step is called.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 if ( $args{'--version'} ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 print $self->appvers() . "\n";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
171 exit 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
172 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
173
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
174 # If we want the galaxy_xml, do that before the reduction step is called.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
175 if ( $args{'--generate_galaxy_xml'} ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
176 require CPT::Galaxy;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
177 my $galaxy_xml_generator = CPT::Galaxy->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
178 $galaxy_xml_generator->gen(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
179 full_options => $parameterCollection,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
180 appdesc => $self->appdesc(),
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
181 appid => $self->appid(),
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
182 appname => $self->appname(),
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 appvers => $self->appvers(),
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
184 defaults => $passed_opts{'defaults'},
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
185 outputs => $passed_opts{'outputs'},
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
186 tests => $passed_opts{'tests'},
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
187 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
188 exit 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
189 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
190
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
191 if( $args{'--gen_test'} ){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
192 require CPT::GenerateTests;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
193 my $tgen = CPT::GenerateTests->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
194 if(defined $passed_opts{'tests'}){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
195 print $tgen->gen(@{$passed_opts{'tests'}});
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
196 }else{
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197 print $tgen->gen_empty();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
198 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
199 exit 0;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
200 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
202 # Now that the options_spec is complete, we reduce to something getopt will be happy with
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 my @getopt_spec = $parameterCollection->getopt();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204 #print STDERR Dumper \@getopt_spec;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205 #exit 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
207 # It would be nice if there was a way to ensure that it didn't die here...
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
208 # Execute getopt
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
209 my ( $local_opt, $usage ) = Getopt::Long::Descriptive::describe_options( $usage_desc, @getopt_spec );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
210 $self->opt($local_opt);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 # Now that we've gotten the user's options, we need to copy their values back to our ParameterCollection
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
213 $parameterCollection->populate_from_getopt($self->opt());
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
214
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 # If they want help, print + exit
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
216 if ( $self->opt && $self->opt->help ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
217 print $usage;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
218 exit 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
219 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220 # Validate their choices
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221 if ( $parameterCollection->validate($self->opt) ) {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
222 return $self->opt;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 # Easy access for the script, don't want them to have to deal with PC (just yet)
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
224 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
225 else {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 # Some params failed to validate, so we die.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 croak "Validation errors were found so cannot continue";
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
228 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
229 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231 no Moose;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
232 1;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
233
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
234 __END__
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 =pod
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
238 =encoding UTF-8
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
239
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 =head1 NAME
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
241
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
242 CPT::GalaxyGetOpt
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
243
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 =head1 VERSION
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
246 version 1.99.4
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
247
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
248 =head2 getOptions
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
249
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
250 my $ggo = CPT::GalaxyGetOpt->new();
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
251 my $options = $ggo->getOptions(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
252 'options' => [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
253 [ 'file', 'Input file', { validate => 'File/Input' } ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
254 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
255 "option" => "Select an option!",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
256 {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
257 validate => 'Option',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
258 options => \%options,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
259 multiple => 1,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
260 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
261 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
262 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
263 "float" => "I'm a float",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
264 { validate => 'Float' }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
265 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
266 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
267 "int" => "I'm an int",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
268 { validate => 'Int', default => [42, 34], required => 1, multiple => 1 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
269 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
270 [],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
271 ['New section'],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
272 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
273 "string" => "I'm a simple string",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
274 { validate => 'String' }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
275 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
276 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
277 'flag' => 'This is a flag',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
278 { validate => 'Flag' }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
279 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
280 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
281 'outputs' => [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
282 [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
283 'my_output_data',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
284 'Output TXT File',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
285 {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
286 validate => 'File/Output',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
287 required => 1,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
288 default => 'out',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
289 data_format => 'text/plain',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
290 default_format => 'TXT',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
291 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
292 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
293 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
294 'defaults' => [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
295 'appid' => 'TemplateScript',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
296 'appname' => 'Template',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
297 'appdesc' => 'A basic template for a new CPT application',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
298 'appvers' => '1.94',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
299 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
300 'tests' => [
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
301 {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
302 test_name => "Default",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
303 params => {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
304 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
305 outputs => {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
306 'my_output_data' => ["out.txt", 'test-data/outputs/template.default.txt' ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
307 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
308 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
309 {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
310 test_name => "Option A specified",
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
311 params => {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
312 'int', '10000',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
313 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
314 outputs => {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
315 'my_output_data' => ["out.txt", 'test-data/outputs/template.A.txt' ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
316 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
317 },
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
318 ],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
319 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
320
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
321 my @data;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
322 foreach(qw(file int string option float flag)){
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
323 # Create a 2D array of all of our optoins
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
324 push(@data, [ $_, $options->{$_}]);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
325 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
326
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
327 my %table = (
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
328 'Sheet1' => {
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
329 header => [qw(Key Value)],
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
330 data => \@data,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
331 }
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
332 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
333
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
334 # And store it to file!
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
335 use CPT::OutputFiles;
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
336 my $crr_output = CPT::OutputFiles->new(
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
337 name => 'my_output_data',
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
338 GGO => $ggo,
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
339 );
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
340 $crr_output->CRR(data => \%table);
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
341
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
342 Gets command line options, and prints docs. Very convenient, removes the burden of writing any Getopt code from you.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
343
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
344 =head3 Default Options Provided
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
345
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
346 =over 4
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
347
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
348 =item *
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
349
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
350 help, man - cause an early exit and printing of the POD for your script.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
351
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
352 =item *
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
353
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
354 verbose - flag to make the script verbose. Will print everything that is sent to returnResults. Individual scripts should take advantage of this option
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
355
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
356 =back
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
357
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
358 =head3 Advanced Options Provided
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
359
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
360 =over 4
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
361
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
362 =item C<--generate_galaxy_xml>
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
363
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
364 Generates valid XML for the tool for use in Galaxy
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
365
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
366 =item C<--gen_test>
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
367
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
368 Generates code to test the script using specified test data
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
369
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
370 =back
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
371
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
372 =head1 AUTHOR
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
373
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
374 Eric Rasche <rasche.eric@yandex.ru>
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
375
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
376 =head1 COPYRIGHT AND LICENSE
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
377
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
378 This software is Copyright (c) 2014 by Eric Rasche.
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
379
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
380 This is free software, licensed under:
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
381
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
382 The GNU General Public License, Version 3, June 2007
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
383
8691c1c61a8e planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
384 =cut