RubyGems - workflow-to-galaxy - Versions diffs - 0.2.9 → 0.3.0 - Mend

workflow-to-galaxy 0.2.9 → 0.3.0

Files changed (23) hide show

data/CHANGES +5 -0
data/README +1 -1
data/Rakefile +5 -10
data/bin/workflow_to_galaxy.rb +58 -65
data/doc/rdoc/CHANGES.html +10 -3
data/doc/rdoc/Generator.html +49 -46
data/doc/rdoc/LICENSE.html +3 -3
data/doc/rdoc/README.html +4 -4
data/doc/rdoc/WorkflowToGalaxy.html +33 -3
data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +338 -0
data/doc/rdoc/WorkflowToGalaxy/Workflows.html +155 -0
data/doc/rdoc/created.rid +6 -7
data/doc/rdoc/index.html +6 -6
data/doc/rdoc/lib/workflow-to-galaxy/constants_rb.html +52 -0
data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +7 -4
data/doc/rdoc/lib/workflow-to-galaxy_rb.html +4 -2
data/lib/workflow-to-galaxy.rb +4 -2
data/lib/workflow-to-galaxy/constants.rb +8 -0
data/lib/workflow-to-galaxy/galaxy.rb +628 -0
metadata +22 -20
data/lib/generator.rb +0 -265
data/lib/workflow-to-galaxy/generator.rb +0 -511
data/lib/workflow_to_galaxy.rb +0 -65

data/doc/rdoc/created.rid CHANGED Viewed

@@ -1,8 +1,7 @@
-Tue, 26 Jul 2011 16:38:29 +0200
-lib/generator.rb	Tue, 26 Jul 2011 16:35:55 +0200
-lib/workflow-to-galaxy.rb	Tue, 26 Jul 2011 16:35:55 +0200
+Thu, 13 Oct 2011 12:56:15 +0200
+lib/workflow-to-galaxy.rb	Thu, 13 Oct 2011 12:51:40 +0200
+lib/workflow-to-galaxy/constants.rb	Mon, 10 Oct 2011 14:10:32 +0200
+lib/workflow-to-galaxy/galaxy.rb	Thu, 13 Oct 2011 12:47:28 +0200
 LICENSE	Tue, 26 Jul 2011 16:35:55 +0200
-lib/workflow_to_galaxy.rb	Tue, 26 Jul 2011 16:35:55 +0200
-README	Tue, 26 Jul 2011 16:35:55 +0200
-CHANGES	Tue, 26 Jul 2011 16:35:55 +0200
-lib/workflow-to-galaxy/generator.rb	Tue, 26 Jul 2011 16:35:55 +0200
+README	Tue, 04 Oct 2011 17:25:08 +0200
+CHANGES	Thu, 13 Oct 2011 12:55:19 +0200

data/doc/rdoc/index.html CHANGED Viewed

@@ -29,7 +29,7 @@
 <p>Konstantinos Karasavvas</p>
 </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
 <td>
-<p>0.2.9</p>
+<p>0.3.0</p>
 </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
 <td>
 <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>
@@ -120,20 +120,20 @@ href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wi
   <h2 id="classes">Classes/Modules</h2>
   <ul>
-    <li class="module"><a href="Generator.html">Generator</a></li>
+    <li class="module"><a href="WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
-    <li class="class"><a href="Object.html">Object</a></li>
+    <li class="class"><a href="WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
-    <li class="module"><a href="WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+    <li class="module"><a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
   </ul>
   <h2 id="methods">Methods</h2>
   <ul>
-      <li><a href="Generator.html#method-i-generate_script">#generate_script &mdash; Generator</a></li>
+      <li><a href="WorkflowToGalaxy/GalaxyTool.html#method-c-new">::new &mdash; WorkflowToGalaxy::GalaxyTool</a></li>
-      <li><a href="Generator.html#method-i-generate_xml">#generate_xml &mdash; Generator</a></li>
+      <li><a href="WorkflowToGalaxy/GalaxyTool.html#method-i-generate">#generate &mdash; WorkflowToGalaxy::GalaxyTool</a></li>
   </ul>

data/doc/rdoc/lib/workflow-to-galaxy/constants_rb.html ADDED Viewed

@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
+  <title>File: constants.rb [workflow-to-galaxy Docs]</title>
+  <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet" />
+  <script src="../../js/jquery.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="../../js/thickbox-compressed.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="../../js/quicksearch.js" type="text/javascript"
+    charset="utf-8"></script>
+  <script src="../../js/darkfish.js" type="text/javascript"
+    charset="utf-8"></script>
+</head>
+<body class="file file-popup">
+  <div id="metadata">
+    <dl>
+      <dt class="modified-date">Last Modified</dt>
+      <dd class="modified-date">Mon Oct 10 14:10:32 +0200 2011</dd>
+      <dt class="requires">Requires</dt>
+      <dd class="requires">
+        <ul>
+        </ul>
+      </dd>
+    </dl>
+  </div>
+  <div id="documentation">
+    <div class="description">
+      <h2>Description</h2>
+    </div>
+  </div>
+</body>
+</html>

data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html CHANGED Viewed

@@ -24,13 +24,19 @@
   <div id="metadata">
     <dl>
       <dt class="modified-date">Last Modified</dt>
-      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
+      <dd class="modified-date">Thu Oct 13 12:25:01 +0200 2011</dd>
       <dt class="requires">Requires</dt>
       <dd class="requires">
         <ul>
+          <li>myexperiment-rest</li>
+          <li>t2flow/model.rb</li>
+          <li>t2flow/parser.rb</li>
         </ul>
       </dd>
@@ -44,9 +50,6 @@
     <div class="description">
       <h2>Description</h2>
-<p>The <a href="../../Generator.html">Generator</a> module contains two public
-methods that generate a Galaxy’s tool XML and script files</p>
     </div>
   </div>

data/doc/rdoc/lib/workflow-to-galaxy_rb.html CHANGED Viewed

@@ -24,14 +24,16 @@
   <div id="metadata">
     <dl>
       <dt class="modified-date">Last Modified</dt>
-      <dd class="modified-date">Tue Jul 26 16:35:55 +0200 2011</dd>
+      <dd class="modified-date">Thu Oct 13 12:51:40 +0200 2011</dd>
       <dt class="requires">Requires</dt>
       <dd class="requires">
         <ul>
-          <li>workflow-to-galaxy/generator</li>
+          <li>workflow-to-galaxy/galaxy</li>
+          <li>workflow-to-galaxy/constants</li>
         </ul>
       </dd>

data/lib/workflow-to-galaxy.rb CHANGED Viewed

@@ -1,5 +1,7 @@
-require 'workflow-to-galaxy/generator'
+require 'workflow-to-galaxy/galaxy'
+require 'workflow-to-galaxy/constants'
-module WorkflowToGalaxy
+module WorkflowToGalaxy  # TODO rename to WorkflowWrappers?
 end

data/lib/workflow-to-galaxy/constants.rb ADDED Viewed

@@ -0,0 +1,8 @@
+module WorkflowToGalaxy
+  module Workflows
+    MYEXPERIMENT_TAVERNA2 = "myexperiment_taverna2"
+    T2FLOW = "t2flow"
+  end
+end

data/lib/workflow-to-galaxy/galaxy.rb ADDED Viewed

@@ -0,0 +1,628 @@
+require 'myexperiment-rest'
+require 't2flow/model.rb'
+require 't2flow/parser.rb'
+module WorkflowToGalaxy
+  include MyExperimentREST
+  #
+  # The _GalaxyTool_ class contains a +generate+ public method that generates the
+  # required files (XML and script) for a Galaxy tool.
+  #
+  class GalaxyTool
+    # +config+ contains data needed in relation to what the tool will do and
+    # +wkf_object+ contains the workflow object that will be used to generate
+    # the galaxy tool
+    attr_accessor :wkf_object, :config
+    # Instantiates a galaxy tool generator.
+    # +config+ is a hash:
+    #
+    # :wkf_source (initial workflow input, see Workflows module)
+    # :params     (a hash with the following parameters -- MYEXPERIMENT_TAVERNA2)
+    #   :t2_server  (the t2 server)
+    #   :url        (the myexperiment workflow URL)
+    #   :xml_out    (the file handle for the generated xml -- optional)
+    #   :rb_out    (the file handle for the generated rb -- optional)
+    #
+    # :params     (a hash with the following parameters -- T2FLOW)
+    #   :t2flow   (the file name and path)
+    #   :xml_out    (the file handle for the generated xml -- optional)
+    #   :rb_out    (the file handle for the generated rb -- optional)
+    #-
+    # TODO: does initialize appear in rdoc? -- these will go to README as well...
+    def initialize(config)
+      @config = config
+    end
+    # private methods
+    private
+    # Used to create indentation when generating code
+    def indent(n)
+      ind = ""
+      n.times { ind += "  "  }
+      ind
+    end
+    # Galaxy's XML tool tag
+    def tool_begin_tag(out, name)
+      out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
+    end
+    # Galaxy's XML command tag
+    def command_tag(out, t2_workflow, script)
+      out.write indent(1) + "<command interpreter=\"ruby\">\n"
+      out.write indent(2) + script + "\n"
+      # inputs
+      t2_workflow.inputs.each do |i|
+        out.write indent(2) + "#if $#{i.name}_source.history_or_textfield == \"textfield\":\n"
+        out.write indent(3) + "false \"$#{i.name}_source.textfield_#{i.name}\"\n"
+        out.write indent(2) + "#else:\n"
+        out.write indent(3) + "true  \"$#{i.name}_source.history_#{i.name}\"\n"
+        out.write indent(2) + "#end if\n"
+      end
+      # results as zip input
+      out.write indent(2) + "$results_as_zip\n"
+      # outputs
+      out.write indent(2)
+      t2_workflow.outputs.each do |o|
+        out.write "$#{o.name} "
+      end
+      # result zip output
+      out.write "$result_zip\n"
+      out.write indent(1) + "</command>\n"
+    end
+    # Galaxy's XML inputs tag
+    def inputs_tag(out, inputs)
+      out.write indent(1) + "<inputs>\n"
+      if inputs.size >= 1
+        inputs.each do |i|
+          out.write indent(2) + "<conditional name=\"#{i.name}_source\">\n"
+          out.write indent(3) + "<param name=\"history_or_textfield\" type=\"select\" label=\"Select source for #{i.name}\">\n"
+          out.write indent(4) + "<option value=\"history\">From history</option>\n"
+          out.write indent(4) + "<option value=\"textfield\" selected=\"true\">Type manually</option>\n"
+          out.write indent(3) + "</param>\n"
+          out.write indent(3) + "<when value=\"history\">\n"
+          out.write indent(4) + "<param name=\"history_#{i.name}\" type=\"data\" label=\"Select #{i.name}\"/>\n"
+          out.write indent(3) + "</when>\n"
+          out.write indent(3) + "<when value=\"textfield\">\n"
+          out.write indent(4) + "<param name=\"textfield_#{i.name}\" type=\"text\" area=\"True\" size=\"2x50\" "
+          if i.examples.size >= 1
+            # escape double quotes characters for galaxy's xml file
+            ex = i.examples[0].to_s.gsub('"', '&quot;')
+            # convert newlines to HTML newlines to display in textareas inputs
+            ex = ex.gsub(/[\n]/, '&#xA;')
+            out.write "value=\"#{ex}\" "
+          end
+          out.write "label=\"Enter #{i.name}\"/>\n"
+          out.write indent(3) + "</when>\n"
+          out.write indent(2) + "</conditional>\n"
+        end
+      else
+        out.write indent(2) + "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
+      end
+      # result as zip input
+      out.write indent(2) + "<param name=\"results_as_zip\" type=\"select\" label=\"Would you also like the raw results as a zip file\">\n"
+      out.write indent(3) + "<option value=\"yes\">Yes</option>\n"
+      out.write indent(3) + "<option value=\"no\" selected=\"true\">No</option>\n"
+      out.write indent(2) + "</param>\n"
+      out.write indent(1) + "</inputs>\n"
+    end
+    # Galaxy's XML outputs tag
+    def outputs_tag(out, outputs)
+      out.write indent(1) + "<outputs>\n"
+      outputs.each do |o|
+        out.write indent(2) + "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
+      end
+      # result zip output
+      out.write indent(2) + "<data format=\"zip\" name=\"result_zip\" label=\"Compressed Results (zip)\">\n"
+      out.write indent(3) + "<filter>results_as_zip == \"yes\"</filter>\n"
+      out.write indent(2) + "</data>\n"
+      out.write indent(1) + "</outputs>\n"
+    end
+    # Galaxy's XML help tag
+    def help_tag(out, t2_workflow)
+      out.write indent(1) + "<help>\n"
+      if t2_workflow.description
+        out.write "**What it does**\n\n"
+        description = t2_workflow.description + "\n\n"
+        # Sometimes the workflow description contains HTML tags that are not allowed
+        # in Galaxy's xml interface specification and thus are removed! Same for
+        # HTML entities!
+        # TODO go through tags and find Galaxy's equivalent to include
+        description.gsub!(/<.*?>|&.*?;/, '')
+        # To remove ^M (cntl-v + cntl-m) characters that DOS files might have
+        description.gsub!(/\r/, '')
+        # TODO that works as a literal too but font changes to courier!
+        #out.write "::\n\n"   # Start Galaxy's literal block to ignore indendation
+        # remove indendation from all description lines since Galaxy is confused by it
+        description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
+        # endline makes the following be parsed as a Galaxy GUI construct
+        out.write "\n"
+      end
+      # if at least one input add it to tool's UI help description
+      if t2_workflow.inputs.size >= 1
+        out.write "-----\n\n"
+        out.write "**Inputs**\n\n"
+        t2_workflow.inputs.each do |i|
+          out.write "- **#{i.name}** "
+          if i.descriptions.size >= 1
+            i.descriptions.each do |desc|
+              out.write desc.to_s + " "
+            end
+          end
+          if i.examples.size >= 1
+            out.write "Examples include:\n\n"
+            i.examples.each do |ex|
+              # some examples have a newline between them that breaks Galaxy's GUI
+              # so we substitute it with ' '
+              #out.write "  - " + ex.to_s.gsub(/[\n]/, ' ') + "\n"
+              # We could substitute them with with &#xA; that works for HTML (e.g. wkf 1180)
+              # But if an example input is truly multiline then input descr. will
+              # display them all as separate inputs...
+              out.write "  - " + ex.to_s.gsub(/[\n]/, '&#xA;  - ') + "\n"
+              # display example inputs as verbatim/literal so it is not our responsibility!!
+              # add indendation after each newline to specify the literal block
+              # TODO this looks ugly if we don't remove all the bullet points!
+              #out.write "::\n\n  " + ex.to_s.gsub(/\n/, '&#xA;  ') + "\n"
+            end
+          end
+          out.write "\n"
+        end
+        out.write "\n"
+      end
+      # if at least one output add it to tool's UI help description
+      if t2_workflow.outputs.size >= 1
+        out.write "-----\n\n"
+        out.write "**Outputs**\n\n"
+        t2_workflow.outputs.each do |o|
+          out.write "- **#{o.name}** "
+          if o.descriptions.size >= 1
+            o.descriptions.each do |desc|
+              out.write desc.to_s + " "
+            end
+          end
+          if o.examples.size >= 1
+            out.write "Examples include:\n\n"
+            o.examples.each do |ex|
+              out.write "  - " + ex.to_s + "\n"
+            end
+          end
+          out.write "\n"
+        end
+        out.write "\n"
+      end
+      out.write "-----\n\n"
+      out.write ".. class:: warningmark\n\n"
+      out.write "**Please note that some workflows are not up-to-date or have dependencies** " <<
+                "that cannot be met by the specific Taverna server that you specified during " <<
+                "generation of this tool. You can make sure that the workflow is valid " <<
+                "by running it in the Taverna Workbench first to confirm that it works " <<
+                "before running it via Galaxy.\n\n"
+      if @config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2
+        out.write "-----\n\n"
+        out.write ".. class:: warningmark\n\n"
+        out.write "**Please note that there might be some repetitions in the workflow description** " <<
+                  "in some of the generated workflows. This is due to a backwards compatibility " <<
+                  "issue on the myExperiment repository which keeps the old descriptions to make " <<
+                  "sure that no information is lost.\n\n"
+        out.write "-----\n\n"
+        out.write ".. class:: infomark\n\n"
+        out.write "**For more information on that workflow please visit** #{t2_workflow.content_uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n\n"
+      end
+      out.write indent(1) + "</help>\n"
+    end
+    # Galaxy's XML tool tag close
+    def tool_end_tag(out)
+      out.write("</tool>\n")
+    end
+    # Galaxy's script preample
+    def script_preample(out)
+      out.write("#!/usr/bin/env ruby\n\n")
+      out.write("# This script can be tested without Galaxy. You can run from the shell as follows:\n#\n")
+      out.write("#   $ script_name.rb <input1> true|false <input2> true|false  yes|no  <output1> <output2>\n#\n")
+      out.write("# After each input value a boolean specifies if the value is literal (false) or if\n")
+      out.write("# it specifies a file name to read as input.\n#\n")
+      out.write("# After all workflow inputs a yes or no input specifies if we also want our results zipped.\n#\n")
+      out.write("# Finally, all the output files follow. Note that if you selected to also get a zip\n")
+      out.write("# then you need to specify an additional output in the end after the normal workflow\n")
+      out.write("# outputs.\n\n")
+      out.write("require 'rubygems'\n")
+      out.write("require 't2-server'\n")
+      out.write("require 'open-uri'\n")
+      out.write("require 'zip/zipfilesystem'\n\n")
+    end
+    # Galaxy's script utility methods
+    # TODO: use ruby's flatten instead of our own !!!
+    def script_util_methods(out)
+      out.write <<'UTIL_METHODS'
+  # sends the zip file to specified output
+  def output_zip_file(uuid, zip_out)
+    File.open("/tmp/#{uuid}.zip") do |zip|
+      while data = zip.read(4096)
+        zip_out.write data
+      end
+    end
+    File.delete("/tmp/#{uuid}.zip")
+  end
+  #
+  # replicates the directory result structure as constructed by the
+  # taverna server and recreates it in a zip File
+  #
+  def add_to_zip_file(output_dir, data_lists, zip_out)
+    zip_out.dir.mkdir("#{output_dir}")
+    data_lists.each_with_index do |item, index|
+      if item.instance_of? Array
+        add_to_zip_file("#{output_dir}/#{index+1}", item, zip_out)
+      else
+        zip_out.file.open("#{output_dir}/#{index+1}", "w") { |f| f.puts item }
+      end
+    end
+  end
+  # method that flattens the list of list of list ... result of get_output
+  def print_flattened_result(out, data_lists)
+    data_lists.each do |l|
+      if l.instance_of? Array
+        print_flattened_result(out, l)
+      else
+        out.puts l
+      end
+    end
+  end
+  #
+  # Method that acquires all the results of the specified output directory.
+  # If valid zip File is passed it also accumulates results as a zip file.
+  #
+  def get_outputs(run, refs, outfile, dir, zip_out=nil)
+    data_lists = run.get_output(dir, refs)
+    print_flattened_result(outfile, data_lists)
+    if zip_out
+      add_to_zip_file(dir, data_lists, zip_out)
+    end
+  end
+  #
+  # Sanitize all special characters in UI inputs that Galaxy substitutes for
+  # security reasons. This methods turns them back to their original values before
+  # using them (i.e. sending them to the taverna server
+  # NB: note that double quote is sanitized to "'" that is because the double code
+  #     confuses the Taverna server ruby library. Apparently, this is not trivial
+  #     to fix.
+  #
+  def sanitize(string)
+    string.gsub(/(__sq__|__dq__|__at__|__cr__|__cn__|__tc__|__gt__|__lt__|__ob__|__cb__|__oc__|__cc__)/) do
+      if $1 == '__sq__'
+        "'"
+      elsif $1 == '__dq__'
+        "'"
+      elsif $1 == '__cr__'
+        "\r"
+      elsif $1 == '__cn__'
+        "\n"
+      elsif $1 == '__tc__'
+        "\t"
+      elsif $1 == '__gt__'
+        '>'
+      elsif $1 == '__lt__'
+        '<'
+      elsif $1 == '__ob__'
+        '['
+      elsif $1 == '__cb__'
+        ']'
+      elsif $1 == '__oc__'
+        '{'
+      elsif $1 == '__cc__'
+        '}'
+      else
+        '@'
+      end
+    end
+  end
+  #
+  # Deletes last new line of file if it exists! It is needed for t2 workflows that
+  # do not sanitize properly, i.e. via a user-provided beanshell script
+  #
+  def chomp_last_newline(file)
+    if File.file?(file) and File.size(file) > 1
+      f = open(file, "rb+")
+      f.seek(-1, File::SEEK_END)
+      f.truncate(File.size(file) - 1) if f.read(1) == "\n"
+      f.close
+    end
+  end
+UTIL_METHODS
+    end
+    # Galaxy's script taverna 2 run
+    def script_create_t2_run(out, wkf, t2_uri)
+      if @config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2
+        out.write "# use the uri reference to download the workflow locally\n"
+        out.write "wkf_file = URI.parse('#{wkf.content_uri}')\n"
+        out.write "in_wkf = open(wkf_file)\n"
+      else     # Workflows::T2FLOW
+        out.write "# uri contains local t2flow file\n"
+        out.write "in_wkf = open('#{wkf.content_uri}')\n"
+      end
+      out.write <<CREATE_T2_RUN
+  wkf = in_wkf.read()
+  # create run
+  begin
+    run = T2Server::Run.create('#{t2_uri}', wkf)
+  rescue T2Server::T2ServerError => e
+    exit 1
+  end
+CREATE_T2_RUN
+    end
+    # Galaxy's script input handling
+    def script_init_inputs(out, t2_workflow)
+      out.write "#\n"
+      out.write "# Get input arguments -- for each input a boolean specifies if it's from history\n"
+      out.write "# thus, for each t2_workflow input we have two arguments in the script!\n"
+      out.write "#\n"
+      t2_workflow.inputs.each_with_index do |input, i|
+        i_name = input.name.to_s
+        out.write "#{i_name}_from_history = ARGV[#{i*2}].chomp\n"
+        out.write "#{i_name}_tmp = ARGV[#{i*2+1}].chomp\n"
+        out.write "if #{i_name}_from_history == \"true\"\n"
+        out.write "  chomp_last_newline(#{i_name}_tmp)\n"
+        out.write "  run.upload_input_file('#{i_name}', #{i_name}_tmp)\n"
+        out.write "else\n"
+        out.write "  run.set_input('#{i_name}', sanitize(#{i_name}_tmp))\n"
+        out.write "end\n"
+      end
+      # add code to handle results_as_zip input, i.e. create zip file
+      out.write "\n# get results_as_zip input and open zip file if appropriate\n"
+      # get argument index after workflow inputs
+      zip_index = t2_workflow.inputs.size * 2
+      out.write "zipped = ARGV[#{zip_index}].chomp == \"yes\"\n"
+      out.write 'zip_out = Zip::ZipFile.open("/tmp/#{run.uuid}.zip", Zip::ZipFile::CREATE) if zipped' + "\n"
+    end
+    # Galaxy's script starting taverna run
+    def script_start_run(out)
+      out.write <<START_RUN
+  # start run and wait until it is finished
+  run.start
+  run.wait(:progress => true)
+START_RUN
+    end
+    # Galaxy's script output handling
+    def script_get_outputs(out, t2_workflow)
+      # outputs start after all inputs plus the results_as_zip input
+      outputs_start_index = t2_workflow.inputs.size * 2 + 1
+      outputs_end_index = outputs_start_index + t2_workflow.outputs.size - 1
+      out.write "# get output arguments and associated them with a file\n"
+      outputs_start_index.upto(outputs_end_index) do |o|
+        out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
+        out.write "begin\n"
+        out.write "  get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + "', zip_out)\n"
+        out.write "rescue Exception => err\n"
+        out.write "  get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + ".error', zip_out)\n"
+        out.write "ensure\n"
+        out.write "  output#{o}.close\n"
+        out.write "end\n"
+      end
+      # close zip file if created when dealing with the inputs
+      #--
+      # ideally that would semantically belong to a separate method
+      out.write "\n# close zip_out (the newly created zip file) if opened\n"
+      out.write "zip_out.close if zip_out\n"
+      # dealing with zip output here -- zip arg index is outputs_end_index (last
+      # output) plus 1
+      out.write "\n# open galaxy zip output and write zip file\n"
+      out.write "if zipped\n"
+      out.write "  galaxy_zip_out = File.open(ARGV[#{outputs_end_index+1}], \"w\")\n"
+      out.write "  output_zip_file(run.uuid, galaxy_zip_out)\n"
+      out.write "  galaxy_zip_out.close\n"
+      out.write "end\n"
+    end
+    # Galaxy's script cleaning taverna run
+    def script_finish_run(out)
+      out.write "\n# delete run\n"
+      out.write "run.delete\n"
+    end
+    # Generates the Galaxy tool's xml file responsible for the UI.
+    # TODO: maybe clean arguments -- only xml_out is needed to be passed
+    def generate_xml(t2_workflow, xml_out)
+      tool_begin_tag(xml_out, xml_out.path.match('([^\/]+)\..*$')[1])
+      command_tag(xml_out, t2_workflow, xml_out.path.match('([^\/]+)\..*$')[1] + '.rb')
+      inputs_tag(xml_out, t2_workflow.inputs)
+      outputs_tag(xml_out, t2_workflow.outputs)
+      help_tag(xml_out, t2_workflow)
+      tool_end_tag(xml_out)
+    end
+    # Generates the Galaxy tool's script file responsible for talking to the
+    # taverna server
+    # TODO: maybe clean arguments -- only xml_out is needed to be passed
+    def generate_rb(t2_workflow, script_out, t2_server)
+      script_preample(script_out)
+      script_util_methods(script_out)
+      script_create_t2_run(script_out, t2_workflow, t2_server)
+      script_init_inputs(script_out, t2_workflow)
+      script_start_run(script_out)
+      script_get_outputs(script_out, t2_workflow)
+      script_finish_run(script_out)
+    end
+    # Populates and returns a _MyExperimentWorkflow_ object (same as in
+    # myexperiment-rest) from a local t2flow file.
+    def populate_taverna_workflow_from_t2flow(t2flow)
+      t2flow_file = File.new(t2flow, "r")
+      parsed_t2flow = T2Flow::Parser.new.parse(t2flow_file)
+      wkf_title = parsed_t2flow.name
+      wkf_descr = parsed_t2flow.main.annotations.descriptions[0]    # gets only the first
+      wkf_uploader_uri = parsed_t2flow.main.annotations.authors[0]
+      wkf_sources = []
+      parsed_t2flow.main.sources.each do |s|
+        wkf_sources << MyExperimentIOData.new(:name => s.name,
+                                              :descriptions => s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
+                                              :examples => s.example_values ? s.example_values : [])
+      end
+      wkf_sinks = []
+      parsed_t2flow.main.sinks.each do |s|
+        wkf_sinks << MyExperimentIOData.new(:name => s.name,
+                                            :descriptions => s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
+                                            :examples => s.example_values ? s.example_values : [])
+      end
+      workflow = MyExperimentWorkflow.new(:content_uri => t2flow,
+                                          :title => wkf_title,
+                                          :description => wkf_descr,
+                                          :inputs => wkf_sources,
+                                          :outputs => wkf_sinks,
+                                          :uploader_uri => wkf_uploader_uri)
+    end
+    # public methods from here onwards
+    public
+    #
+    # Generates the two files needed for a Galaxy tool: a configuration
+    # file (XML) and a processing file (in our case a ruby script)
+    #
+    # :call-seq:
+    #   GalaxyTool.generate() -> nil
+    #
+    def generate
+      # check the type of workflow source and acquire the appropriate data
+      if(config[:wkf_source] == Workflows::MYEXPERIMENT_TAVERNA2)
+        # TODO: check and add auth stuff -- even more unsafe with session cookies
+        # since the myexp username/passwd will be saved in the galaxy ruby script
+        # for all to see...
+        begin
+          # Get workflow data from myexperiment -- a _MyExperimentWorkflow_ object is returned
+          @wkf_object = MyExperimentREST::Workflow.from_uri(@config[:params][:url])
+        rescue Exception => e
+          raise "Problem acquiring workflow data from myExperiment!\n" + e
+        end
+      elsif(config[:wkf_source] == Workflows::T2FLOW)
+        begin
+          # Get workflow data from t2flow file -- a _MyExperimentWorkflow_ object is returned
+          @wkf_object = populate_taverna_workflow_from_t2flow(@config[:params][:t2flow])
+        rescue Exception => e
+          raise "Problem acquiring workflow data from t2flow file!\n" + e
+        end
+      else
+        raise "No such workflow source supported!"
+      end
+      # if an xml_out file handler was not given provide one with the title as the value
+      if @config[:params][:xml_out]
+        generate_xml(@wkf_object, @config[:params][:xml_out])
+      else
+        xml_out = open(@wkf_object.title + ".xml", "w")
+        generate_xml(@wkf_object, xml_out)
+        xml_out.close
+      end
+      # if an rb_out file handler was not given provide one with the title as the value
+      if @config[:params][:rb_out]
+        generate_rb(@wkf_object, @config[:params][:rb_out], @config[:params][:t2_server])
+      else
+        rb_out = open(@wkf_object.title + ".rb", "w")
+        generate_rb(@wkf_object, rb_out, @config[:params][:t2_server])
+        rb_out.close
+      end
+    end
+  end  # class GalaxyTool
+end  # module