Shuttle Run Test

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...

Test::TempDatabase is a Perl module for temporary database creation and destruction. SYNOPSIS use Test::TempDatabase; my $td = Test::TempDatabase->create(dbname => temp_db); my $dbh = $td->handle; ... some tests ... # Test::TempDatabase drops database This module automates creation...


Platforms: *nix

Test::URI is a Perl module that can check Uniform Resource Identifiers (URIs). SYNOPSIS use Test::More tests => 5; use Test::URI; # http://www.example.com:8080/index.html#name uri_scheme_ok( $uri, http ); uri_host_ok( $uri, www.example.com ); uri_port_ok( $uri, 8080 ); uri_path_ok(...


Platforms: *nix

Test::ISBN is a Perl module to check international standard book numbers. SYNOPSIS use Test::More tests => 1; use Test::ISBN; isbn_ok( $isbn ); Functions isbn_ok( STRING ) Ok is the STRING is a valid ISBN, in any format that Business::ISBN accepts. This function only checks the...


Platforms: *nix

Test::Data is a Perl module to test functions for particular variable types. SYNOPSIS use Test::Data qw(Scalar Array Hash Function); Test::Data provides utility functions to check properties and values of data and variables. Functions Plug-in modules define functions for each data type....


Platforms: *nix

Test::WWW::Accessibility is a Perl module to test web pages for accessibility..


Platforms: *nix

Test::Chunks is a Data Driven Testing Framework. NOTE - This module has been deprecated and replaced by Test::Base. This is basically just a renaming of the module. Test::Chunks was not the best name for this module. Please discontinue using Test::Chunks and switch to Test::Base. Helpful Hint:...


Platforms: *nix

Test::Parser is a collection of parsers for different test output file formats. These parse the data into a general purpose data structure that can then be used to create reports, do post-processing analysis, etc. Test-Parser can also export tests in SpikeSources TRPI test description XML...


Platforms: *nix

Test::Parser is a collection of parsers for different test output file formats. These parse the data into a general purpose data structure that can then be used to create reports, do post-processing analysis, etc. Test::Parser can also export tests in SpikeSources TRPI test description XML...


Platforms: *nix

Test::Unit::tests::AllTests is a unit testing framework self tests. SYNOPSIS # command line style use perl TestRunner.pl Test::Unit::tests::AllTests # GUI style use perl TkTestRunner.pl Test::Unit::tests::AllTests This class is used by the unit testing framework to encapsulate all the...


Platforms: *nix

Test::Unit::Tutorial is a Perl module that contains a tutorial on unit testing. SYNOPSIS perldoc Test::Unit::Tutorial Here should be extensive documentation on what unit testing is, why it is useful, and how to do it with the Test::Unit collection of modules. Sorry for not implementing...


Platforms: *nix

Test::Unit::TestSuite is a unit testing framework base class. SYNOPSIS use Test::Unit::TestSuite; # more code here ... sub suite { my $class = shift; # create an empty suite my $suite = Test::Unit::TestSuite->empty_new("A Test Suite"); # get and add an existing suite...


Platforms: *nix

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db...


Platforms: *nix

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model. Parameters: align2model (String) run (String) Run name db (Sequence) Sequences to align (-db) model_file (InFile) Model (-i) pipe:...


Platforms: *nix

Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...


Platforms: *nix

Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init...


Platforms: *nix

Test::Unit::InnerClass is a unit testing framework helper class. SYNOPSIS This class is not intended to be used directly This class is used by the framework to emulate the anonymous inner classes feature of Java. It is much easier to port Java to Perl using this class..


Platforms: *nix

PSA::Test::Builder is a backend for building test libraries. SYNOPSIS package My::Test::Module; use PSA::Test::Builder; require Exporter; @ISA = qw(Exporter); @EXPORT = qw(ok); my $Test = Test::Builder->new; $Test->output(my_logfile); sub import { my($self) = shift; my $pack =...


Platforms: *nix

WebInject is a free tool for automated testing of web applications and services. It can be used to test individual system components that have HTTP interfaces (JSP, ASP, CGI, PHP, Servlets, HTML Forms, etc), and can be used as a test harness to create a suite of [HTTP level] automated functional,...


Platforms: *nix