Hi Dan,

Thanks for the reply and the suggestions. I think the data libraries would
work much better than the get_microbial_data tool as then it would be more
easily kept up to date.

Cheers,

Simon.

On 30 April 2015 at 01:01, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> The <code> tag won’t be going away any time soon, but in many cases there
> are other ways to do what this tag does, using the built-in dynamic options
> (in particular, currently for tab-delimited files), that are much
> preferred. So it is deprecated, and it should be used sparingly, but there
> are times when there isn’t a better way for tools to dynamically build
> their options without using a code file.
>
> In the case of the get microbial data tool, if it was working prior to
> 15.03, it should still be working, afaik we haven’t changed the handling of
> these recently (with the exception of not loading them inside of a ToolShed
> application instance).  Its been a while since I’ve played with that
> specific tool (and we deprecated it ourselves and removed it from main), so
> I can’t confirm off-the-cuff whether it should still be working or not. If
> something really did break with respect to the code files, we should take a
> look though.
>
>
> I think using a Data Library is the perfect replacement for for the
> microbial import tool, and would cause less file duplication when used. But
> what exactly is no longer working?
>
>
> Thanks for using Galaxy,
>
> Dan
>
> On Apr 29, 2015, at 10:38 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
> > On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman
> > <simon.glad...@unimelb.edu.au> wrote:
> >> Hi dev,
> >>
> >> Now that the <code> tagset is deprecated, how do we replace that
> >> functionality. For example the "get microbial data" tool runs the script
> >> listed in the <code> tagset to load the list of available microbe data
> when
> >> the tool is selected. This doesn't seem to work in the latest stable
> 15.03.1
> >> or 15.03.2.
> >>
> >> How do we configure tools like this now? Or is there an updated version
> of
> >> the microbial_import tool?
> >>
> >> Cheers,
> >>
> >> Simon.
> >
> > Good question Simon.
> >
> > I am still using <code> for advanced parameter validation, e.g.
> >
> https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml
> >
> > i.e. Validation before the job gets submitted to the cluster or run.
> > If the <code> tag suddenly goes away, my tool will still work but
> > would be a little less user friendly (some errors would only be
> > spotted after the tool starts running).
> >
> > Peter
> > ___________________________________________________________
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>
>


-- 
Simon Gladman | Bioinformatician
Victorian Life Sciences Computation Initiative - LSCC
187 Grattan Street, The University of Melbourne | Victoria 3010 Australia
T +61 3 9035 5822 | M 0418 421 077
Mail: simon.glad...@unimelb.edu.au
Web: http://www.vlsci.org.au
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