Bio::Tools::Run::PiseWorkflow Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods.
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Bio::Tools::Run::PiseWorkflow Tags

Perl module workflow Pise workflow Pise application objects Pise

Bio::Tools::Run::PiseWorkflow Description

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. 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 workflow's 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(); Requirements: · Perl

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