IIRC then you can change the order of tools manually by copying around the 
individual tools in shed_tool_conf.xml
In my case it builds the integrated_tool_panel.xml in reverse order within the 
section.

I still have labels between the section defined in the tool_conf.xml.
But no subsections.

best,
ido

On Sep 16, 2013, at 6:40 AM, yulia.arzha...@csiro.au wrote:

> Hello guys,
>  
> After porting our Galaxy tools into a tool shed repository the tool sections 
> got lost. I know there is a possibility to assign a repository to a section 
> inside the tools panel when the repository is getting installed. However, we 
> would still like to have sections inside the repository – that makes 
> navigating the tools much neater. Also, the way shed_tool_conf.xml is 
> populated with tools during repository installation seems arbitrary to me. Is 
> there any way to control this, to have repository tools sorted/displayed in a 
> certain order in Tools panel, in the very least, alphabetically? I’ve got 
> many tools in my repository (and no, it is not possible to divide them into 
> several repositories), and the way they are sorted or divided into sections 
> makes navigating the tools much easier for a user.
> Thanks,
> Yulia
>  
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