# $Id: einverted.pm,v 1.6 2006/07/04 22:23:34 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::einverted
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::PiseApplication::einverted
=head1 SYNOPSIS
#
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::einverted
Bioperl class for:
EINVERTED Finds DNA inverted repeats (EMBOSS)
Parameters:
(see also:
for available values):
einverted (String)
init (String)
sequence (Sequence)
sequence -- dna [single sequence] (-sequence)
pipe: seqfile
gap (Integer)
Gap penalty (-gap)
threshold (Integer)
Minimum score threshold (-threshold)
match (Integer)
Match score (-match)
mismatch (Integer)
Mismatch score (-mismatch)
maxrepeat (Integer)
Maximum extent of repeats (-maxrepeat)
outfile (OutFile)
outfile (-outfile)
auto (String)
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
=head1 AUTHOR
Catherine Letondal (letondal@pasteur.fr)
=head1 COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 SEE ALSO
=over
=item *
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tools::Run::PiseApplication);
=head2 new
Title : new()
Usage : my $einverted = Bio::Tools::Run::PiseApplication::einverted->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::einverted object.
This method should not be used directly, but rather by
a Bio::Tools::Run::AnalysisFactory::Pise instance.
my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
my $einverted = $factory->program('einverted');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::einverted.
=cut
sub new {
my ($class, $location, $email, @params) = @_;
my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/einverted.pm
$self->{COMMAND} = "einverted";
$self->{VERSION} = "5.a";
$self->{TITLE} = "EINVERTED";
$self->{DESCRIPTION} = "Finds DNA inverted repeats (EMBOSS)";
$self->{OPT_EMAIL} = 0;
$self->{CATEGORIES} = [
"nucleic:repeats",
"nucleic:2d structure",
];
$self->{_INTERFACE_STANDOUT} = undef;
$self->{_STANDOUT_FILE} = undef;
$self->{TOP_PARAMETERS} = [
"einverted",
"init",
"input",
"required",
"advanced",
"output",
"auto",
];
$self->{PARAMETERS_ORDER} = [
"einverted",
"init",
"input", # input Section
"sequence", # sequence -- dna [single sequence] (-sequence)
"required", # required Section
"gap", # Gap penalty (-gap)
"threshold", # Minimum score threshold (-threshold)
"match", # Match score (-match)
"mismatch", # Mismatch score (-mismatch)
"advanced", # advanced Section
"maxrepeat", # Maximum extent of repeats (-maxrepeat)
"output", # output Section
"outfile", # outfile (-outfile)
"auto",
];
$self->{TYPE} = {
"einverted" => 'String',
"init" => 'String',
"input" => 'Paragraph',
"sequence" => 'Sequence',
"required" => 'Paragraph',
"gap" => 'Integer',
"threshold" => 'Integer',
"match" => 'Integer',
"mismatch" => 'Integer',
"advanced" => 'Paragraph',
"maxrepeat" => 'Integer',
"output" => 'Paragraph',
"outfile" => 'OutFile',
"auto" => 'String',
};
$self->{FORMAT} = {
"init" => {
"perl" => ' "" ',
},
"input" => {
},
"sequence" => {
"perl" => '" -sequence=$value -sformat=fasta"',
},
"required" => {
},
"gap" => {
"perl" => '" -gap=$value"',
},
"threshold" => {
"perl" => '" -threshold=$value"',
},
"match" => {
"perl" => '" -match=$value"',
},
"mismatch" => {
"perl" => '" -mismatch=$value"',
},
"advanced" => {
},
"maxrepeat" => {
"perl" => '(defined $value && $value != $vdef)? " -maxrepeat=$value" : ""',
},
"output" => {
},
"outfile" => {
"perl" => '" -outfile=$value"',
},
"auto" => {
"perl" => '" -auto -stdout"',
},
"einverted" => {
"perl" => '"einverted"',
}
};
$self->{FILENAMES} = {
};
$self->{SEQFMT} = {
"sequence" => [8],
};
$self->{GROUP} = {
"init" => -10,
"sequence" => 1,
"gap" => 2,
"threshold" => 3,
"match" => 4,
"mismatch" => 5,
"maxrepeat" => 6,
"outfile" => 7,
"auto" => 8,
"einverted" => 0
};
$self->{BY_GROUP_PARAMETERS} = [
"init",
"input",
"advanced",
"required",
"output",
"einverted",
"sequence",
"gap",
"threshold",
"match",
"mismatch",
"maxrepeat",
"outfile",
"auto",
];
$self->{SIZE} = {
};
$self->{ISHIDDEN} = {
"init" => 1,
"input" => 0,
"sequence" => 0,
"required" => 0,
"gap" => 0,
"threshold" => 0,
"match" => 0,
"mismatch" => 0,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 0,
"auto" => 1,
"einverted" => 1
};
$self->{ISCOMMAND} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"gap" => 0,
"threshold" => 0,
"match" => 0,
"mismatch" => 0,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 0,
"auto" => 0,
};
$self->{ISMANDATORY} = {
"init" => 0,
"input" => 0,
"sequence" => 1,
"required" => 0,
"gap" => 1,
"threshold" => 1,
"match" => 1,
"mismatch" => 1,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 1,
"auto" => 0,
};
$self->{PROMPT} = {
"init" => "",
"input" => "input Section",
"sequence" => "sequence -- dna [single sequence] (-sequence)",
"required" => "required Section",
"gap" => "Gap penalty (-gap)",
"threshold" => "Minimum score threshold (-threshold)",
"match" => "Match score (-match)",
"mismatch" => "Mismatch score (-mismatch)",
"advanced" => "advanced Section",
"maxrepeat" => "Maximum extent of repeats (-maxrepeat)",
"output" => "output Section",
"outfile" => "outfile (-outfile)",
"auto" => "",
};
$self->{ISSTANDOUT} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"gap" => 0,
"threshold" => 0,
"match" => 0,
"mismatch" => 0,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 0,
"auto" => 0,
};
$self->{VLIST} = {
"input" => ['sequence',],
"required" => ['gap','threshold','match','mismatch',],
"advanced" => ['maxrepeat',],
"output" => ['outfile',],
};
$self->{FLIST} = {
};
$self->{SEPARATOR} = {
};
$self->{VDEF} = {
"gap" => '12',
"threshold" => '50',
"match" => '3',
"mismatch" => '-4',
"maxrepeat" => '4000',
"outfile" => 'outfile.out',
};
$self->{PRECOND} = {
"init" => { "perl" => '1' },
"input" => { "perl" => '1' },
"sequence" => { "perl" => '1' },
"required" => { "perl" => '1' },
"gap" => { "perl" => '1' },
"threshold" => { "perl" => '1' },
"match" => { "perl" => '1' },
"mismatch" => { "perl" => '1' },
"advanced" => { "perl" => '1' },
"maxrepeat" => { "perl" => '1' },
"output" => { "perl" => '1' },
"outfile" => { "perl" => '1' },
"auto" => { "perl" => '1' },
};
$self->{CTRL} = {
};
$self->{PIPEOUT} = {
};
$self->{WITHPIPEOUT} = {
};
$self->{PIPEIN} = {
"sequence" => {
"seqfile" => '1',
},
};
$self->{WITHPIPEIN} = {
};
$self->{ISCLEAN} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"gap" => 0,
"threshold" => 0,
"match" => 0,
"mismatch" => 0,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 0,
"auto" => 0,
};
$self->{ISSIMPLE} = {
"init" => 0,
"input" => 0,
"sequence" => 1,
"required" => 0,
"gap" => 1,
"threshold" => 1,
"match" => 1,
"mismatch" => 1,
"advanced" => 0,
"maxrepeat" => 0,
"output" => 0,
"outfile" => 1,
"auto" => 0,
};
$self->{PARAMFILE} = {
};
$self->{COMMENT} = {
"maxrepeat" => [
"Maximum separation between the start of repeat and the end of the inverted repeat (the default is 4000 bases).",
],
};
$self->{SCALEMIN} = {
};
$self->{SCALEMAX} = {
};
$self->{SCALEINC} = {
};
$self->{INFO} = {
};
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/einverted.pm
$self->_init_params(@params);
return $self;
}
1; # Needed to keep compiler happy