> >> Unfortunately, I can't help much with refresh_on_change either, we just
> >> use the <conditional>/<when> tag set. I have been under the impression
> >> the the documentation has been written for 'refresh_on_change' in the
> >> meantime. I am sorry, I should have checked first, before suggesting it.
> > 
> > No problem. I’ll know to keep en eye for documentation on this
> > feature :)
> 
> refresh_on_change is not a feature that is exposed to tool developers
> for use in tool wrappers. Instead, it's used behind the scenes to
> make conditional/when and dynamic options tags work.

Hmmm, ok. That explains why there are so few uses of it.
May I suggest amending 
<http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cpage.3E_tag_set>
to make it clearer that tool developers are not meant to use it?

> >> Regarding the command line: you can have different commandlines,
> >> eg
> >> 
> >>   <command>
> >>     #if   ($summary.mode=="a")#commandline1
> >>     #elif ($summary.mode=="b")#commandline2
> >>     #elif ($summary.mode=="c")#commandline3
> >>     #end if
> >>   </command>
> >> 
> >> and one of those 'commandlines' could be two commands (ie indexing
> >> first, followed by the next binary)
> > 
> > I had not thought of that! That makes sense, yes. I’ll do that.
> 
> Frequently, if/else is used to progressively build a command line:
> 
> --
> my_script.py
> 
> #if option1:
>       --enable-option1 --option1-parameter $option1-parameter
> #elif option2:
>       --enable-option1 --option1-parameter $option1-parameter
> #endif

Sure. I meant I had not thought of executing *several* commands in the 
<command> tag.

Thanks,

Jean-Frédéric

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