Initial pass at allowing the setting of certain metadata parameters on upload (controlled via a flag). This allows the user to specify the 'base_name' to be used for Rgenetics datatypes, etc. Bunch of cleanup needed in upload.

tools/data_source/upload.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 
-<tool name="Upload File" id="upload1" version="1.0.1">
+<tool name="Upload File" id="upload1" version="1.0.2">
   <description>
     from your computer  
   </description>
@@ -15,7 +15,7 @@
       </options>
     </param>
     <param name="async_datasets" type="hidden" value="None"/>
-    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type">
+    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
       <param name="file_data" type="file" size="30" label="File" ajax-upload="true">
         <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
       </param>
@@ -25,6 +25,7 @@
       </param>
     </upload_dataset>
     <param name="dbkey" type="genomebuild" label="Genome" />
+    <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
     <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
   </inputs>
   <help>