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’, $input.dbkey, ‘path’)}
Finally, I like your indexing syntax, and it would be great to use something like that in place of the explicit method call above.
Best,
J.
--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University
Hi,
I'm working on tool wrapper that needs three reference genome locations (2bit/lastz, all_fasta and novoalign). Is there a way to fetch the three paths from the loc files using a single select box? I've looked around in a couple of tool wrappers on the toolshed, but could find any leads. Something like the following would be ok:
Select options from all_fasta.loc
-> upon change, set hidden variables to novoalign.loc + lastz_seqs.loc using a filter tag or something against the selected options from all_fasta.
Even more simple : access in the command tag like:
--novoidx novoalign-loc.options[dbkey=$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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
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