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Bio::Tools::Run::PiseWorkflow 1.4

  Date Added: March 15, 2010  |  Visits: 1.149

Bio::Tools::Run::PiseWorkflow

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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();.

Requirements: No special requirements
Platforms: Linux
Keyword: Application Application Objects Biotoolsrunpiseworkflow Create Create A Libraries Method Pise Piseworkflow Programming To Create Using Workflow
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License: Freeware Size: 829.44 KB
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