I'm writing a galaxy tool xml file for an in house existing R script. I have a 
conditional parameter set for selecting the dataset to work with but I would 
like to access the path of the file from the data table I've created:

  <table name="cri_datasets" comment_char="#">
      <columns>value, name, path</columns>
      <file path="tool-data/cri/datasets.loc" />

Here is the beginning of the xml file:

  <command interpreter="R --vanilla --slave -f">
    rp.R --args $dataset.name.fields.name $dataset.name.fields.path $input 
$column $output_txt  $output_html $output_html.files_path $dataset.outcome 
$dataset.receptor $dataset.treatment $dataset.er $dataset.age $dataset.grade 
$dataset.signature $dataset.margins $dataset.groups $dataset.gleason 
$dataset.tstage 2&gt;stderr || cat stderr 1&gt;&amp;2

    <param name="input" type="data" format="tabular,txt" label="Source file" 
help="File containing a list of gene symbols"/>
    <param name="column" type="data_column" data_ref="input" numerical="False" 
label="Column" help="Column containing gene symbols (only available for tabular 
input file)" />
    <conditional name="dataset">
      <param name="name" type="select" label="Dataset">
        <options from_data_table="cri_datasets" />

but when running the tool, here is the error message I get:

Traceback (most recent call last):
  File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/runners/local.py", line 
59, in run_job
  File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/__init__.py", line 429, 
in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py", line 1971, 
in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/opt/local/home/webapp/galaxy/lib/galaxy/util/template.py", line 9, in 
    return str( Template( source=template_text, searchList=[context] ) )
 line 1004, in __str__
    return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
NotFound: cannot find 'fields' while searching for 'dataset.name.fields.name'

Is it possible to access the other columns of a loc file? It seems possible 
based of what I read on the wiki 
 using from_data_table and syntax of ${param.fields.path} but I could not 
manage to make it work. 

Any help would be very much appreciated. Thanks!
Kind regards,

Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)1223 404 334

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