There's an as-yet undocumented method that you can use to get arbitrary fields 
in a loc file:

__get_data_table_entry__(<table_name>, <key_field>, <field_value>, 
<value_field>)

So for the novoalign entry you could do:

--novoidx ${__get_data_table_entry__(‘novoalign’, ‘dbkey’, $input.dbkey, 
‘path’)}

Finally, I like your indexing syntax, and it would be great to use something 
like that in place of the explicit method call above.

Best,
J.

--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University



On Jul 27, 2014, at 10:44 AM, Geert Vandeweyer 
<geert.vandewey...@uantwerpen.be> wrote:

> Hi,
> 
> I'm working on tool wrapper that needs three reference genome locations 
> (2bit/lastz, all_fasta and novoalign). Is there a way to fetch the three 
> paths from the loc files using a single select box? I've looked around in a 
> couple of tool wrappers on the toolshed, but could find any leads. Something 
> like the following would be ok:
> 
> Select options from all_fasta.loc
>    -> upon change, set hidden variables to novoalign.loc + lastz_seqs.loc 
> using a filter tag or something against the selected options from all_fasta.
> 
> Even more simple : access in the command tag like:
>   --novoidx novoalign-loc.options[dbkey=$input.dbkey,path] --fasta 
> all_fasta-loc[dbkey=$input.dbkey,path] etc , using the dbkey from the input 
> file (which is a bam file in this case)
> 
> In this case, error handling should come from the tool, if one of the indices 
> is missing.
> 
> I'm currently using three selection boxes, but that looks a but redundant to 
> the user, as they all have to select the same thing.
> 
> Best,
> 
> Geert
> 
> -- 
> 
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
> 
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