If I understand you correctly, would this mean generating a custom .loc file for this tool containing the concatenated paths? Or can I concatenate paths from different .loc files somehow, which would allow me to use the default loc files?


On 07/28/2014 09:33 AM, Hans-Rudolf Hotz wrote:
Hi Geert

A simple solution might be: you hand over a string containing all three paths to your wrapper, and then the wrapper splits the string into the three individual paths.


On 07/27/2014 04:44 PM, Geert Vandeweyer wrote:

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.




Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be

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