workflow-to-galaxy 0.2.9 → 0.3.0

data/CHANGES

@@ -1,5 +1,10 @@
 = Changes log for the Taverna-Galaxy Gem
 
+== Version 0.3.0
+* Updated to newer myexperiment-rest lib (0.3.0).
+* Restructured, now more modular and extensible.
+
+
 == Version 0.2.9
 * Fixed minor bug when workflow had empty description
 * Added instructions to generated scripts on how to run them without Galaxy.

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.2.9
+Gem Version:: 0.3.0
 Contact::     mailto:kostas.karasavvas@nbic.nl
 Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
 Copyright::   (c) 2010 Netherlands Bioinformatics Centre, The Netherlands

data/Rakefile

@@ -1,8 +1,3 @@
-# 
-# To change this template, choose Tools | Templates
-# and open the template in the editor.
- 
-
 require 'rubygems'
 require 'rake'
 require 'rake/clean'
@@ -12,7 +7,7 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 'workflow-to-galaxy'
-  s.version = '0.2.9'
+  s.version = '0.3.0'
   s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
   s.summary = 'This script acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (.xml and .rb files).'
   s.description = s.summary
@@ -22,10 +17,10 @@ spec = Gem::Specification.new do |s|
   s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
   s.require_path = "lib"
   s.bindir = "bin"
-  s.add_dependency 'myexperiment-rest', '>= 0.2.6'
-  s.add_dependency 'taverna-t2flow', '>= 0.2.0'
-  s.add_dependency 't2-server', '>= 0.5.3'
-  s.add_dependency 'rubyzip', '>= 0.9.4'
+  s.add_dependency 'myexperiment-rest', '~> 0.3.0'
+  s.add_dependency 'taverna-t2flow', '~> 0.2.0'
+  s.add_dependency 't2-server', '~> 0.6.1'
+  s.add_dependency 'rubyzip', '~> 0.9.4'
 end
 
 Gem::PackageTask.new(spec) do |p|

data/bin/workflow_to_galaxy.rb

@@ -2,40 +2,10 @@
 
 require 'rubygems'
 require 'optparse'
-require 't2flow/model.rb'
-require 't2flow/parser.rb'
 require 'cgi'
-require 'myexperiment-rest'
 require 'workflow-to-galaxy'
 
-include MyExperimentREST
-include Generator
-
-
-# Populates and returns a _TavernaWorkflow_ 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_sources = []
-  parsed_t2flow.main.sources.each do |s|
-    wkf_sources << TavernaIOData.new(s.name, 
-                                     s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
-                                     s.example_values ? s.example_values : [])
-  end
-  wkf_sinks = []
-  parsed_t2flow.main.sinks.each do |s|
-    wkf_sinks << TavernaIOData.new(s.name,
-                                   s.descriptions ? CGI.escapeHTML(s.descriptions.to_s) : [],
-                                   s.example_values ? s.example_values : [])
-  end
-
-  workflow = TavernaWorkflow.new(TavernaWorkflow::T2_FLOW, t2flow, wkf_title, wkf_descr, wkf_sources, wkf_sinks)
-
-end
+include WorkflowToGalaxy
 
 
 # Set up and parse arguments
@@ -43,21 +13,24 @@ out_file = ""
 t2_server = ""
 options = {}
 opts = OptionParser.new do |opt|
-  opt.banner = "Usage: workflow_to_galaxy [options] <myExperiement-workflow> | <t2flow-file>"
+  opt.banner = "Usage: workflow_to_galaxy [options] <myExperiment-workflow> | <t2flow-file>"
   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. Alternatively "
-  opt.separator "a t2flow file can be passed for workflows not in myExperiment. 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|
+  opt.separator "specified Taverna2 workflow, where <myExperiment-workflow> is the full "
+  opt.separator "URL of the workflow in the myExperiment website. Alternatively a t2flow "
+  opt.separator "file can be passed for workflows not in myExperiment. Available options "
+  opt.separator "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|
+  opt.on("-s SERVER", "--server=SERVER", "The taverna server that the script will",
+                                         "request execution from. If not specified",
+                                         "'http://localhost:8080/taverna-server'",
+                                         "will be used.") do |val|
     t2_server = val if val != nil
   end
 
@@ -75,36 +48,56 @@ if url == nil
   exit 1
 end
 
-# Object to store the workflow object
-wkf_data = nil
+# Set taverna server if not specified
+t2_server ||= "http://localhost:8080/taverna-server"
 
-if options[:t2flow]
-  # Parse local t2flow file -- a _Taverna_Workflow_ object is returned
-  wkf_data = populate_taverna_workflow_from_t2flow(url)
-else
-  # Get workflow data from myexperiment -- a _Taverna_Workflow_ object is returned
-  wkf_data = Workflows.new.read(url)
-end
 
-# Set output files
+#if options[:t2flow]
+#  wkf_source =
+#else
+#  wkf_source = Workflows::MYEXPERIMENT_TAVERNA2
+#end
+
+# create file handlers
 if out_file != ""
-  xml_file = "#{out_file}.xml"
-  script_file = "#{out_file}.rb"
-else
-  xml_file = "#{wkf_data.title}".gsub(/\W/, '') + ".xml"
-  script_file = "#{wkf_data.title}".gsub(/\W/, '') + ".rb"
+  xml_out = open("#{out_file}.xml", "w")
+  rb_out = open("#{out_file}.rb", "w")
 end
 
-# Set taverna server if not specified
-t2_server = "http://localhost:8980/taverna-server"  if t2_server == ""
 
+# create generator or wrapper (could have used url for t2flow key to avoid
+# if/else but future sources would still need them)
+if options[:t2flow]
+  if out_file != ""
+    wkf = GalaxyTool.new(:wkf_source => Workflows::T2FLOW,
+                         :params => {:t2_server => t2_server,
+                                     :t2flow => url,
+                                     :xml_out => xml_out,
+                                     :rb_out => rb_out } )
+  else
+    wkf = GalaxyTool.new(:wkf_source => Workflows::T2FLOW,
+                         :params => {:t2_server => t2_server,
+                                     :t2flow => url } )
+  end
+else
+  if out_file != ""
+    wkf = GalaxyTool.new(:wkf_source => Workflows::MYEXPERIMENT_TAVERNA2,
+                         :params => {:t2_server => t2_server,
+                                     :url => url,
+                                     :xml_out => xml_out,
+                                     :rb_out => rb_out } )
+  else
+    wkf = GalaxyTool.new(:wkf_source => Workflows::MYEXPERIMENT_TAVERNA2,
+                         :params => {:t2_server => t2_server,
+                                     :url => url } )
+  end
+end
 
+# close file handlers
+if out_file != ""
+  xml_out.close
+  rb_out.close
+end
 
-# Generate Galaxy tool's files
-xml_file_ob = File.open(xml_file, "w")
-generate_xml(wkf_data, xml_file, xml_file_ob)
-xml_file_ob.close
+wkf.generate
 
-script_file_ob = File.open(script_file, "w")
-generate_script(wkf_data, t2_server, script_file_ob)
-script_file_ob.close

data/doc/rdoc/CHANGES.html

@@ -64,11 +64,11 @@
 
         <ul class="link-list">
         
-          <li><a href="./Generator.html">Generator</a></li>
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
-          <li><a href="./Object.html">Object</a></li>
+          <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
         
-          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+          <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
@@ -82,6 +82,13 @@
     
 <h1>Changes log for the Taverna-Galaxy Gem</h1>
 
+<h2>Version 0.3.0</h2>
+<ul><li>
+<p>Updated to newer myexperiment-rest lib (0.3.0).</p>
+</li><li>
+<p>Restructured, now more modular and extensible.</p>
+</li></ul>
+
 <h2>Version 0.2.9</h2>
 <ul><li>
 <p>Fixed minor bug when workflow had empty description</p>

data/doc/rdoc/Generator.html

@@ -34,9 +34,6 @@
         <div class="section-body">
           <ul>
           
-            <li><a href="./lib/generator_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
-              class="thickbox" title="lib/generator.rb">lib/generator.rb</a></li>
-          
             <li><a href="./lib/workflow-to-galaxy/generator_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
               class="thickbox" title="lib/workflow-to-galaxy/generator.rb">lib/workflow-to-galaxy/generator.rb</a></li>
           
@@ -105,8 +102,6 @@
         
           <li><a href="./Generator.html">Generator</a></li>
         
-          <li><a href="./Object.html">Object</a></li>
-        
           <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
         </ul>
@@ -122,9 +117,6 @@
 
     <div id="description" class="description">
       
-<p>Contains code to generate the Galaxy’s tool xml and script files</p>
-<hr style="height: 1px">
-
 <p>The <a href="Generator.html">Generator</a> module contains two public
 methods that generate a Galaxy’s tool XML and script files</p>
 
@@ -137,19 +129,6 @@ methods that generate a Galaxy’s tool XML and script files</p>
       
 
       
-      <!-- Constants -->
-      <div id="constants-list" class="section">
-        <h3 class="section-header">Constants</h3>
-        <dl>
-        
-          <dt><a name="INDENT">INDENT</a></dt>
-          
-          <dd class="description"></dd>
-          
-        
-        </dl>
-      </div>
-      
 
       
 
@@ -163,33 +142,45 @@ methods that generate a Galaxy’s tool XML and script files</p>
           <a name="method-i-generate_script"></a>
 
           
+          
           <div class="method-heading">
-            <span class="method-name">generate_script</span><span
-              class="method-args">(me_rest, t2_server, script_file)</span>
+            <span class="method-callseq">generate_script(my_exp_rest, t2_server, script_file) &rarr; nil</span>
+            
             <span class="method-click-advice">click to toggle source</span>
+            
           </div>
           
+          
 
           <div class="method-description">
             
             <p>Generates the Galaxy tool’s script file responsible for talking to the
 taverna server</p>
+<dl class="rdoc-list"><dt><tt>my_exp_rest</tt></dt>
+<dd>
+<p>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST.ReadWorkflow.new(url)</em></p>
+</dd><dt><tt>t2_server</tt></dt>
+<dd>
+<p>a string containing the URL of the taverna 2 server</p>
+</dd><dt><tt>script_out</tt></dt>
+<dd>
+<p>the file handler to write the generated script code</p>
+</dd></dl>
             
 
             
             <div class="method-source-code" id="generate_script-source">
 <pre>
-<span class="ruby-comment"># File lib/generator.rb, line 253</span>
-<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">me_rest</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_file</span>)
-  <span class="ruby-identifier">out</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">script_file</span>, <span class="ruby-string">&quot;w&quot;</span>)
-  <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">out</span>)
-  <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">out</span>)
-  <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">t2_server</span>)
-  <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
-  <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">out</span>)
-  <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
-  <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">out</span>)
-  <span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/generator.rb, line 501</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>)
+  <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">script_out</span>)
+  <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">script_out</span>)
 <span class="ruby-keyword">end</span></pre>
             </div><!-- generate_script-source -->
             
@@ -205,31 +196,43 @@ taverna server</p>
           <a name="method-i-generate_xml"></a>
 
           
+          
           <div class="method-heading">
-            <span class="method-name">generate_xml</span><span
-              class="method-args">(me_rest, xml_file)</span>
+            <span class="method-callseq">generate_xml(my_exp_rest, xml_file) &rarr; nil</span>
+            
             <span class="method-click-advice">click to toggle source</span>
+            
           </div>
           
+          
 
           <div class="method-description">
             
             <p>Generates the Galaxy tool’s xml file responsible for the UI.</p>
+<dl class="rdoc-list"><dt><tt>t2_workflow</tt></dt>
+<dd>
+<p>a <em>Workflow</em> object as returned from
+<em>MyExperimentREST::Workflows.new.read(url)</em></p>
+</dd><dt><tt>xml_file</tt></dt>
+<dd>
+<p>a string containing the name of the generated XML file</p>
+</dd><dt><tt>xml_out</tt></dt>
+<dd>
+<p>the file handler to write the generated XML tags</p>
+</dd></dl>
             
 
             
             <div class="method-source-code" id="generate_xml-source">
 <pre>
-<span class="ruby-comment"># File lib/generator.rb, line 238</span>
-<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">me_rest</span>, <span class="ruby-identifier">xml_file</span>)
-  <span class="ruby-identifier">out</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">xml_file</span>, <span class="ruby-string">&quot;w&quot;</span>)
-  <span class="ruby-identifier">tool_b</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">title</span>)
-  <span class="ruby-identifier">command_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>, <span class="ruby-identifier">xml_file</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-string">'.xml'</span>, <span class="ruby-string">'.rb'</span>))
-  <span class="ruby-identifier">inputs_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">inputs</span>)
-  <span class="ruby-identifier">outputs_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>.<span class="ruby-identifier">workflow</span>.<span class="ruby-identifier">outputs</span>)
-  <span class="ruby-identifier">help_be</span>(<span class="ruby-identifier">out</span>, <span class="ruby-identifier">me_rest</span>)
-  <span class="ruby-identifier">tool_e</span>(<span class="ruby-identifier">out</span>)
-  <span class="ruby-identifier">out</span>.<span class="ruby-identifier">close</span>
+<span class="ruby-comment"># File lib/workflow-to-galaxy/generator.rb, line 482</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>, <span class="ruby-identifier">xml_out</span>)
+  <span class="ruby-identifier">tool_begin_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">title</span>)
+  <span class="ruby-identifier">command_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-string">'.xml'</span>, <span class="ruby-string">'.rb'</span>))
+  <span class="ruby-identifier">inputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">inputs</span>)
+  <span class="ruby-identifier">outputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">outputs</span>)
+  <span class="ruby-identifier">help_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>)
+  <span class="ruby-identifier">tool_end_tag</span>(<span class="ruby-identifier">xml_out</span>)
 <span class="ruby-keyword">end</span></pre>
             </div><!-- generate_xml-source -->
             

data/doc/rdoc/LICENSE.html

@@ -64,11 +64,11 @@
 
         <ul class="link-list">
         
-          <li><a href="./Generator.html">Generator</a></li>
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
-          <li><a href="./Object.html">Object</a></li>
+          <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
         
-          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+          <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>

data/doc/rdoc/README.html

@@ -64,11 +64,11 @@
 
         <ul class="link-list">
         
-          <li><a href="./Generator.html">Generator</a></li>
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
-          <li><a href="./Object.html">Object</a></li>
+          <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
         
-          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+          <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>
@@ -86,7 +86,7 @@
 <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>

data/doc/rdoc/WorkflowToGalaxy.html

@@ -34,6 +34,12 @@
         <div class="section-body">
           <ul>
           
+            <li><a href="./lib/workflow-to-galaxy/galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/workflow-to-galaxy/galaxy.rb">lib/workflow-to-galaxy/galaxy.rb</a></li>
+          
+            <li><a href="./lib/workflow-to-galaxy/constants_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
+              class="thickbox" title="lib/workflow-to-galaxy/constants.rb">lib/workflow-to-galaxy/constants.rb</a></li>
+          
             <li><a href="./lib/workflow-to-galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
               class="thickbox" title="lib/workflow-to-galaxy.rb">lib/workflow-to-galaxy.rb</a></li>
           
@@ -50,10 +56,34 @@
       
 
       
+      <!-- Namespace Contents -->
+      <div id="namespace-list-section" class="section">
+        <h3 class="section-header">Namespace</h3>
+        <ul class="link-list">
+          
+          <li><span class="type">MODULE</span> <a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
+          
+          <li><span class="type">CLASS</span> <a href="WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
+          
+        </ul>
+      </div>
+      
 
       
 
       
+      <!-- Included Modules -->
+      <div id="includes-section" class="section">
+        <h3 class="section-header">Included Modules</h3>
+        <ul class="link-list">
+        
+        
+          <li><span class="include">MyExperimentREST</span></li>
+        
+        
+        </ul>
+      </div>
+      
     </div>
 
     <div id="project-metadata">
@@ -88,11 +118,11 @@
 
         <ul class="link-list">
         
-          <li><a href="./Generator.html">Generator</a></li>
+          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
         
-          <li><a href="./Object.html">Object</a></li>
+          <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
         
-          <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
+          <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
         
         </ul>
         <div id="no-class-search-results" style="display: none;">No matching classes.</div>