Hi Hans-Rudolf,

Thank you for your answer.

> > I am not sure of the best design here.
> > *Providing another wrapperfor this other binary, with users
> > explicitly
> > using it beforehand in their workflow?
> > *Assuming the databases have been processed outside of Galaxy
> > beforehand
> > ? (As the tool relies on the file name, this would work for
> > databases in
> > the .loc file but not ones from the history)
> > *Providing an extra-smart wrapper which would check if the database
> > has
> > been indexed, and if not invisibly indexing before running
> > SortMeRNA ?
> >
> or providing an extra-flexible wrapper (and its corresponding UI
> defined in the XML file): You first ask the question whether the database is
> in the history (indexed or to be indexed) or in the local files system.
> Then depending on the choice, the UI changes according the three
> options.
> There are several ways to offer a dynamic UI, eg:
> <conditional>/<when>
> tag sets, <page> tag set or possibilities with the
> "refresh_on_change"
> option.

I see. Actually, I already implemented the UI change to ask whether the 
database is selected from local file system or history tab, using <conditional> 
(just like in the fimo.xml wrapper). I am a bit confused about the 
refresh_on_change, is there any documentation on it? The only working example I 
see in the tools is the rgManQQ.xml wrapper, where it is used jointly with 
dynamic_options (same question about doc?). This seems to be handy ; but unless 
I am mistaken it seems it can only work with a <code>, right? But the <code> 
tag is deprecated, and the doc is unclear about the replacement to use. 
<actions> seems to only work for <output> data, right?

Also, I am directly calling the binary in the <command>. If I understand you 
correctly, it would be easier to hae an additional Python wrapper, which would 
pre-index the database is needed or asked. Is that correct?

> > Am I missing something, or the <stdio><regex> is not meant to be
> > used this way?
> You should get the complete error message when you click on the 'bug' icon.

When clicking on the bug icon, Galaxy tells me “Either this dataset does not 
exist or you do not have permission to access it.” (but that may be a problem 
with my local Galaxy instance I guess)

> I don't think this is possible without having it just next to Alpha.

I see, thanks. 

> I hope this helps

It does, thanks!


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