workflow-to-galaxy 0.2.9 → 0.3.0

data/lib/workflow_to_galaxy.rb

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