workflow-to-galaxy 0.2.9 → 0.3.0

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@@ -1,65 +0,0 @@
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- #!/usr/bin/env ruby
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-
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- require 'rubygems'
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- require 'optparse'
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- require 'myexperiment-rest'
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- require 'generator'
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-
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- include MyExperimentREST
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- include Generator
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-
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-
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- # Set up and parse arguments
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- out_file = ""
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- t2_server = ""
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- opts = OptionParser.new do |opt|
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- opt.banner = "Usage: workflow_to_galaxy [options] <myExperiement-workflow>"
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- opt.separator ""
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- opt.separator "Generates a Galaxy tool (a UI xml definition plus a script) for the "
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- opt.separator "specified Taverna2 workflow, where <myExperiment-workflow> is "
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- opt.separator "the full URL of the workflow in the myExperiment website. Available "
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- opt.separator "options are:"
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-
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- opt.on("-o OUTPUT", "--output=OUTPUT", "The file name(s) of the generated tool. " +
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- "If it is not specified then the workflow's name will be used.") do |val|
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- out_file = val if val != nil
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- end
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-
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- opt.on("-s SERVER", "--server=SERVER", "The taverna server that the script will request execution from. " +
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- "If it is not specified then 'http://localhost:8980/taverna-server' will be used.") do |val|
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- t2_server = val if val != nil
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- end
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- end
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-
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- opts.parse!
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-
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- # Read and check workflow URL
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- url = ARGV.shift
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- if url == nil
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- puts opts
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- exit 1
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- end
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-
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- # Get workflow data from myexperiment
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- me_rest = ReadWorkflow.new(url)
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-
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- # Set output files
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- if out_file != ""
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- xml_file = "#{out_file}.xml"
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- script_file = "#{out_file}.rb"
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- else
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- xml_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".xml"
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- script_file = "#{me_rest.workflow.title}".gsub(/\W/, '') + ".rb"
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- end
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-
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- # Set taverna server
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- if t2_server == ""
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- t2_server = "http://localhost:8980/taverna-server"
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- end
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-
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-
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-
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- generate_xml(me_rest, xml_file)
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- generate_script(me_rest, t2_server, script_file)
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-
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-