Hi,

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" />
  </table>

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
  </command>

  <inputs>
    <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" />
      </param>
...

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
    job_wrapper.prepare()
  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 
fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File 
"/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
 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 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coptions.3E_tag_set
 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.

--
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



NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-named 
person(s). If you are not the intended recipient, notify the sender 
immediately, delete this email from your system and do not disclose or use for 
any purpose. 

We may monitor all incoming and outgoing emails in line with current 
legislation. We have taken steps to ensure that this email and attachments are 
free from any virus, but it remains your responsibility to ensure that viruses 
do not adversely affect you. 
Cancer Research UK
Registered in England and Wales
Company Registered Number: 4325234.
Registered Charity Number: 1089464 and Scotland SC041666
Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to