diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 6c1670487f5..1be2811b9e1 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -89,9 +89,10 @@ class Configuration( object ):
             raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir )
         # Configuration options for taking advantage of nginx features
         self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
-        self.nginx_upload_location = kwargs.get( 'nginx_upload_store', False )
-        if self.nginx_upload_location:
-            self.nginx_upload_location = os.path.abspath( self.nginx_upload_location )
+        self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False )
+        self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
+        if self.nginx_upload_store:
+            self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
         # Parse global_conf and save the parser
         global_conf = kwargs.get( 'global_conf', None )
         global_conf_parser = ConfigParser.ConfigParser()
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index cf341b17737..4f03768fdf4 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -464,7 +464,11 @@ class Tool:
         if input_elem:
             # Handle properties of the input form
             self.check_values = util.string_as_bool( input_elem.get("check_values", "true") )
-            self.action = input_elem.get( "action", "/tool_runner/index")
+            self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) )
+            if self.nginx_upload and self.app.config.nginx_upload_path:
+                self.action = input_elem.get( "action", self.app.config.nginx_upload_path + "?nginx_redir=/tool_runner/index" )
+            else:
+                self.action = input_elem.get( "action", "/tool_runner/index")
             self.target = input_elem.get( "target", "galaxy_main" )
             self.method = input_elem.get( "method", "post" )
             # Parse the actual parameters
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
index c2e45d94456..dbf3f950c42 100644
--- a/lib/galaxy/tools/actions/upload_common.py
+++ b/lib/galaxy/tools/actions/upload_common.py
@@ -23,6 +23,8 @@ def persist_uploads( params ):
                 f.file.close()
                 upload_dataset['file_data'] = dict( filename = f.filename,
                                                     local_filename = local_filename )
+            elif type( f ) == dict and 'filename' and 'local_filename' not in f:
+                raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' )
             if upload_dataset['url_paste'].strip() != '':
                 upload_dataset['url_paste'] = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" )[0]
             else:
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 9790ded96db..3bfbc8dc495 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -304,22 +304,21 @@ class FileToolParameter( ToolParameter ):
     def get_html_field( self, trans=None, value=None, other_values={}  ):
         return form_builder.FileField( self.name, ajax = self.ajax, value = value )
     def from_html( self, value, trans=None, other_values={} ):
-        # TODO: Fix nginx upload module support
         # Middleware or proxies may encode files in special ways (TODO: this
         # should be pluggable)
-        #if type( value ) == dict:
-        #    upload_location = self.tool.app.config.nginx_upload_location
-        #    assert upload_location, \
-        #        "Request appears to have been processed by nginx_upload_module \
-        #        but Galaxy is not configured to recgonize it"
-        #    # Check that the file is in the right location
-        #    local_filename = os.path.abspath( value['path'] )
-        #    assert local_filename.startswith( upload_location ), \
-        #        "Filename provided by nginx is not in correct directory"
-        #    value = Bunch(
-        #        filename = value["name"],
-        #        local_filename = local_filename
-        #    )
+        if type( value ) == dict:
+            upload_store = self.tool.app.config.nginx_upload_store
+            assert upload_store, \
+                "Request appears to have been processed by nginx_upload_module \
+                but Galaxy is not configured to recognize it"
+            # Check that the file is in the right location
+            local_filename = os.path.abspath( value['path'] )
+            assert local_filename.startswith( upload_store ), \
+                "Filename provided by nginx is not in correct directory"
+            value = dict(
+                filename = value["name"],
+                local_filename = local_filename
+            )
         return value
     def get_required_enctype( self ):
         """
diff --git a/lib/galaxy/web/controllers/library.py b/lib/galaxy/web/controllers/library.py
index 1bbdf9fd8aa..de0442d6725 100644
--- a/lib/galaxy/web/controllers/library.py
+++ b/lib/galaxy/web/controllers/library.py
@@ -792,8 +792,13 @@ class Library( BaseController ):
             # Send the current history to the form to enable importing datasets from history to library
             history = trans.get_history()
             history.refresh()
+            # If we're using nginx upload, override the form action
+            action = web.url_for( controller='library', action='library_dataset_dataset_association' )
+            if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
+                action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
             return trans.fill_template( '/library/upload.mako',
                                         upload_option=upload_option,
+                                        action=action,
                                         library_id=library_id,
                                         folder_id=folder_id,
                                         replace_dataset=replace_dataset,
diff --git a/lib/galaxy/web/controllers/library_admin.py b/lib/galaxy/web/controllers/library_admin.py
index 6865f395d17..ca1fbd7193d 100644
--- a/lib/galaxy/web/controllers/library_admin.py
+++ b/lib/galaxy/web/controllers/library_admin.py
@@ -487,8 +487,13 @@ class LibraryAdmin( BaseController ):
             # Send the current history to the form to enable importing datasets from history to library
             history = trans.get_history()
             history.refresh()
+            # If we're using nginx upload, override the form action
+            action = web.url_for( controller='library_admin', action='library_dataset_dataset_association' )
+            if upload_option == 'upload_file' and trans.app.config.nginx_upload_path:
+                action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action
             return trans.fill_template( '/admin/library/upload.mako',
                                         upload_option=upload_option,
+                                        action=action,
                                         library_id=library_id,
                                         folder_id=folder_id,
                                         replace_dataset=replace_dataset,
diff --git a/templates/admin/library/upload.mako b/templates/admin/library/upload.mako
index 14a5c9fed70..3c5ec1c4e71 100644
--- a/templates/admin/library/upload.mako
+++ b/templates/admin/library/upload.mako
@@ -32,4 +32,4 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-${render_upload_form( 'library_admin', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
+${render_upload_form( 'library_admin', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
diff --git a/templates/library/library_dataset_common.mako b/templates/library/library_dataset_common.mako
index f78c39232c1..5e12404a771 100644
--- a/templates/library/library_dataset_common.mako
+++ b/templates/library/library_dataset_common.mako
@@ -1,4 +1,4 @@
-<%def name="render_upload_form( controller, upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )">
+<%def name="render_upload_form( controller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )">
     <% import os, os.path %>
     %if upload_option in [ 'upload_file', 'upload_directory' ]:
         <div class="toolForm" id="upload_library_dataset">
@@ -8,7 +8,7 @@
                 <div class="toolFormTitle">Upload a directory of files</div>
             %endif
             <div class="toolFormBody">
-                <form name="upload_library_dataset" action="${h.url_for( controller=controller, action='library_dataset_dataset_association' )}" enctype="multipart/form-data" method="post">
+                <form name="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post">
                     <input type="hidden" name="tool_id" value="upload1"/>
                     <input type="hidden" name="tool_state" value="None"/>
                     <input type="hidden" name="library_id" value="${library_id}"/>
diff --git a/templates/library/upload.mako b/templates/library/upload.mako
index 3993ca8d3fb..2e8a161a8a8 100644
--- a/templates/library/upload.mako
+++ b/templates/library/upload.mako
@@ -32,4 +32,4 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-${render_upload_form( 'library', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
+${render_upload_form( 'library', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )}
diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 81756f52f88..60f55be9c74 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -14,7 +14,7 @@
         ${output.dataset.dataset.id}:${output}
     #end while
   </command>
-  <inputs>
+  <inputs nginx_upload="true">
     <param name="file_type" type="select" label="File Format" help="Which format? See help below">
       <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
         <column name="value" index="1"/>