Hi Greg,

Thanks for the tips. A validator would indeed be great as I made the changes 
you suggested but still it did not solve the issue (the tool still does not 
appear - so probably yet another mistake is there...).

Regards,

Pieter.

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: donderdag 24 oktober 2013 17:29
To: Lukasse, Pieter
Cc: 'Peter Cock'; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents

Hello Pieter,

There are 2 different issues in 2 of your xml files that make them invalid XML.




1. In your tool_dependencies.xml file, you need to close the version string 
attribute in the <package> tag. So the following line with the problem:

<package name="xtandem" version="12.10011>

is fixed when it looks like this:

<package name="xtandem" version="12.10011">




2. In your mass comb_dbsearch_xtandem.xml file, the comment outside of the 
</tool> tag on the last line problematic.

</tool>
<!--  NB: edit /etc/profile and add the xtandem bin folder to PATH -->

The above XML results in the XML document being parsed such that the XML root 
is the comment itself.  If you move the comment line insideo of the <tool> tag 
set, all is well:

<!--  NB: edit /etc/profile and add the xtandem bin folder to PATH -->
</tool>




Unfortunartely, it is difficult to render meaningful messages for invalid XML 
like this as the XMNL parser does not provide much of anything meaningful that 
can be passed on in the UI.  At some point I may find the chance to incorporate 
a validator, but just don't currently have the time.

Greg Von Kuster



On Oct 24, 2013, at 10:46 AM, "Lukasse, Pieter" 
<pieter.luka...@wur.nl<mailto:pieter.luka...@wur.nl>> wrote:


Hi Peter,

I've added the package to the test toolshed now as well, but there the revision 
is not seen in the metadata (see screenshot). What is needed to get this 
repository "active"? Is this still the "reset metadata" (is this a bug or by 
design)? Thanks for your help!


<image001.jpg>

Regards,

Pieter.

-----Original Message-----
From: Peter Cock [mailto:p.j.a.c...@googlemail.com<http://googlemail.com>]
Sent: donderdag 24 oktober 2013 13:27
To: Lukasse, Pieter
Cc: Greg Von Kuster (g...@bx.psu.edu<mailto:g...@bx.psu.edu>); 
galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] Tool refuses to appear in Toolshed package contents

On Thu, Oct 24, 2013 at 12:09 PM, Lukasse, Pieter 
<pieter.luka...@wur.nl<mailto:pieter.luka...@wur.nl>> wrote:
>
> Hi ,
>
> I have a toolshed repository where I expect 5 tools to appear in the
> "Contents of this repository" section but one of them fails to appear
> in the list (see screenshot). Where can I find out what is going
> wrong?
>
> Thanks,
>
> Pieter.


Hi Pieter,

The first thing to confirm is if the missing tool a valid XML file?

Next, does it work in your Galaxy instance (if installed manually).

Now if this problem is only in the Tool Shed, which toolshed is it in?
Your own local tool shed, the main Penn State public Tool Shed, the Penn State 
Test Tool Shed, or somewhere else? If it is your own tool shed, you should be 
able to look at its logging for clues.
If it is a public tool shed, please share the URL for the repository.

Regards,

Peter

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