Bio::Tools::Run::PiseWorkflow 1.4

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::AnalysisFactory::Pise();
# Then create the application objects (Pise::Run::Tools::PiseApplication):
my $clustalw = $factory->program(clustalw);
$clustalw->infile($my_alignment_file);
my $protpars = $factory->program(protpars);

# You can specify different servers for different applications :
my $protdist = $factory->program(protpars
-remote => http://kun.homelinux.com/cgi-bin/Pise/5.a//protpars.pl,
-email => your_email);

# Create a new workflow object :
my $workflow = Bio::Tools::Run::PiseWorkflow->new();

# Define the workflows methods using the application objects:
# the application method $protpars will receive the output of
# type readseq_ok_alig from the application method $clustalw.
$workflow->addpipe(-method => $clustalw,
-tomethod => $protpars,
-pipetype => readseq_ok_alig);

# The application method $clustalw will be piped to a second
# application method ($protdist) using the output of type readseq_ok_alig.
$workflow->addpipe(-method => $clustalw,
-tomethod => $protdist,
-pipetype => readseq_ok_alig);

# The application method $protpars will be piped to the application
# method $consense using the output of type phylip_tree.
my $consense = $factory->program(consense);
$workflow->addpipe(-method => $protpars,
-tomethod => $consense,
-pipetype => phylip_tree);

# Run the workflow.
$workflow->run();