Hi Peter, see below...

On Sep 20, 2012, at 9:43 AM, Peter Cock wrote:

> On Thu, Sep 20, 2012 at 2:16 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Peter,
>> 
>> On Sep 20, 2012, at 5:53 AM, Peter Cock wrote:
>> 
>>> Hi all,
>>> 
>>> I'd like to check (before I try this), if is this expected to work or not?
>>> 
>>> For the normal tool wrappers, is it possible to rename the XML
>>> file (but leave the tool ID inside the XML file unchanged), and
>>> have this *just work* (TM) when automatically updated via the
>>> ToolShed?
>> 
>> Yes, this is possible (and works), but make sure to do the following:
>> 
>> 1. Do not change the tool ID string nor the tool version string,
>> just rename the tool config.
>> 2. Make sure to upload the change as a tarball, and keep the
>> following select list checked as "Yes".  This means that you
>> need to have everything in your tarball that you want to keep.
>> The old tool config will be eliminated and the new, renamed
>> one will replace it.  Since the tool id and version remain the
>> same, the "valid / installable" changeset revision will be reset
>> to the new tip.
>> 
> 
> OK. What would happen if I did the rename and increased
> the version number in one step (which seems the most
> common situation)?


Assuming you want to increase the version number of the tool, this is fine.  
However, the version number should be changed only if the tool's behavior has 
changed such that different results are produced (from the previous version) if 
the same analysis is executed.  Just changing the name of the tool config 
should not result in a new version of the tool.  

This is important because changing the version of the tool will result in a new 
installable changeset revision being set, which means that if someone installed 
the previous installable changeset revision (that included the old version of 
the tool), they will need to install the new revision rather than bein able to 
just get updates to the one previously installed.  This behavior ensures that 
each version of a tool can be installed, ensuring reproducibility over time.


> 
>>> 
>>> Similarly, for the new 'blast_datatypes' Tool Shed entry, can
>>> I rename xml.py which defines the file format(s) to something
>>> like ncbi_blast.py (and update the datatypes_conf.xml
>>> ToolShed file to match)? My desire here is partly to avoid
>>> the current namespace clash with galaxy.datatypes.xml
>>> but also that I intend this to include other non-XML BLAST
>>> formats as well (e.g. BLAST database).
>> 
>> This change should pose no problems.  As you state, just
>> make sure to change the repository's datatypes_conf.xml
>> file accordingly.
> 
> Excellent - I'll try to do that rename operation today for the
> BLAST datatypes.
> 
> Peter


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