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Documentation updates, as well as location parameter, continuing with…
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… programs starting by h, i, k, l and m.

svn path=/bioperl-run/trunk/; revision=13466
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letondal committed Jun 10, 2003
1 parent 5e162d3 commit 91684c0
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97 changes: 79 additions & 18 deletions Bio/Tools/Run/PiseApplication/helixturnhelix.pm
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Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
# $Id$
# BioPerl module for Bio::Tools::Run::PiseApplication::helixturnhelix
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME
Expand All @@ -15,25 +23,22 @@ Bio::Tools::Run::PiseApplication::helixturnhelix
HELIXTURNHELIX Report nucleic acid binding motifs (EMBOSS)
Parameters:
Parameters:
helixturnhelix (String)
(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/helixturnhelix.html
for available values):
init (String)
helixturnhelix (String)
input (Paragraph)
input Section
init (String)
sequence (Sequence)
sequence -- PureProtein [sequences] (-sequence)
pipe: seqsfile
advanced (Paragraph)
advanced Section
mean (Float)
Mean value (-mean)
Expand All @@ -46,14 +51,68 @@ Bio::Tools::Run::PiseApplication::helixturnhelix
eightyseven (Switch)
Use the old (1987) weight data (-eightyseven)
output (Paragraph)
output Section
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/MailList.shtml - 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
email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
=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 *
http://bioweb.pasteur.fr/seqanal/interfaces/helixturnhelix.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut

Expand All @@ -69,20 +128,20 @@ use Bio::Tools::Run::PiseApplication;
=head2 new
Title : new()
Usage : my $helixturnhelix = Bio::Tools::Run::PiseApplication::helixturnhelix->new($remote, $email, @params);
Usage : my $helixturnhelix = Bio::Tools::Run::PiseApplication::helixturnhelix->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::helixturnhelix object.
This method should not be used directly, but rather by
a Bio::Factory::Pise instance:
my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
a Bio::Tools::Run::AnalysisFactory::Pise instance.
my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
my $helixturnhelix = $factory->program('helixturnhelix');
Example :
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::helixturnhelix.
=cut

sub new {
my ($class, $remote, $email, @params) = @_;
my $self = $class->SUPER::new($remote, $email);
my ($class, $location, $email, @params) = @_;
my $self = $class->SUPER::new($location, $email);

# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/helixturnhelix.pm

Expand All @@ -92,6 +151,8 @@ sub new {

$self->{DESCRIPTION} = "Report nucleic acid binding motifs (EMBOSS)";

$self->{OPT_EMAIL} = 0;

$self->{CATEGORIES} = [

"protein:2d structure",
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99 changes: 80 additions & 19 deletions Bio/Tools/Run/PiseApplication/hmmalign.pm
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Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
# $Id$
# BioPerl module for Bio::Tools::Run::PiseApplication::hmmalign
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME
Expand All @@ -15,11 +23,15 @@ Bio::Tools::Run::PiseApplication::hmmalign
HMMER hmmalign - align sequences to an HMM profile (S .Eddy)
Parameters:
Parameters:
(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/hmmalign.html
for available values):
hmmalign (String)
hmmalign (String)
seqfile (Sequence)
Sequences File
Expand All @@ -29,29 +41,76 @@ Bio::Tools::Run::PiseApplication::hmmalign
HMM file
pipe: hmmer_HMM
align_file (Results)
pipe: hmmer_alig
output_format (Switch)
Additional output in GCG MSF format (default is SELEX format)
msf_align_file (Results)
pipe: readseq_ok_alig
match_states (Switch)
Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. (-m)
expert_options (Paragraph)
Expert Options
mapali (String)
(--mapali f)
withali (String)
(--withali f)
=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/MailList.shtml - 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
email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
=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 *
http://bioweb.pasteur.fr/seqanal/interfaces/hmmalign.html
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut

#'
Expand All @@ -66,20 +125,20 @@ use Bio::Tools::Run::PiseApplication;
=head2 new
Title : new()
Usage : my $hmmalign = Bio::Tools::Run::PiseApplication::hmmalign->new($remote, $email, @params);
Usage : my $hmmalign = Bio::Tools::Run::PiseApplication::hmmalign->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::hmmalign object.
This method should not be used directly, but rather by
a Bio::Factory::Pise instance:
my $factory = Bio::Factory::Pise->new(-email => 'me@myhome');
a Bio::Tools::Run::AnalysisFactory::Pise instance.
my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
my $hmmalign = $factory->program('hmmalign');
Example :
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::hmmalign.
=cut

sub new {
my ($class, $remote, $email, @params) = @_;
my $self = $class->SUPER::new($remote, $email);
my ($class, $location, $email, @params) = @_;
my $self = $class->SUPER::new($location, $email);

# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/hmmalign.pm

Expand All @@ -89,6 +148,8 @@ sub new {

$self->{DESCRIPTION} = "hmmalign - align sequences to an HMM profile";

$self->{OPT_EMAIL} = 0;

$self->{AUTHORS} = "S .Eddy";

$self->{_INTERFACE_STANDOUT} = undef;
Expand Down
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