Tool XML Question - using option/from_file name in 'label' - galaxy-user

22 Nov 2008


      Hello,
I have a tool which has an <option> with 'from_file' attribute:
...
     <param name="database" type="select" label="Mapping Database">
             <options from_file="mapping_filter_databases.txt">
                 <column name="name" index="1"/>
                 <column name="value" index="0"/>
             </options>
     </param>
...
I want to use the database name in the label of the output dataset:
   <outputs>
       <data format="fasta"
      name="output_mapped" label="Mappers of $input.name to $database" />
   </outputs>
The '$database' variables is replaced with the database's filename (the 
'value' column). I'd like it to be the 'name' column, but using 
"$database.name" throws an runtime exception:
      NotFound: cannot find 'name' while searching for 'database.name'
(full backtrace is listed below).
Is there a way to display the name instead of the value in an <option> 
clause ?
Thanks!
    Gordon.
URL: http://tango/tool_runner/index
File 
'build/bdist.solaris-2.11-i86pc/egg/weberror/evalexception/middleware.py', 
line 364 in respond
File 'build/bdist.solaris-2.11-i86pc/egg/paste/debug/prints.py', line 98 
in __call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/wsgilib.py', line 539 in 
intercept_output
File 'build/bdist.solaris-2.11-i86pc/egg/beaker/session.py', line 103 in 
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/recursive.py', line 80 in 
__call__
File 'build/bdist.solaris-2.11-i86pc/egg/paste/httpexceptions.py', line 
632 in __call__
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/framework/base.py', 
line 126 in __call__
   body = method( trans, **kwargs )
File 
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/web/controllers/tool_runner.py', 
line 45 in index
   template, vars = tool.handle_input( trans, params.__dict__ )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py', 
line 708 in handle_input
   out_data = self.execute( trans, incoming=params )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/__init__.py', 
line 915 in execute
   return self.tool_action.execute( self, trans, incoming=incoming, 
set_output_hid=set_output_hid )
File 
'/media/sdb1/galaxy/galaxy_devel/lib/galaxy/tools/actions/__init__.py', 
line 159 in execute
   data.name = fill_template( output.label, context=params )
File '/media/sdb1/galaxy/galaxy_devel/lib/galaxy/util/template.py', line 
9 in fill_template
   return str( Template( source=template_text, searchList=[context] ) )
File '<string>', line 28 in respond
NotFound: cannot find 'name' while searching for 'database.name'