Hello Peter, On Jul 4, 2011, at 11:20 AM, Peter Cock wrote:

Hi all,

I've noticed some inconsistencies in the new tool shed. First of all the table view uses "Name" and "Description" for fields shown as "Name" and "Synopsis" on the tool details page.

Fixed in the next update to the tool sheds - thanks.

Also the field "Name" is not showing the tool name or tool suite name - they are showing the tool or tool suite ID.

This is because the "Name" field is the name of the repository, not the name of 1 or more tools within it. Keep in mind that there is not a 1-1 mapping of repository and Galaxy tool or suite of tools. A repository may include items like exported Galaxy workflows, but possibly no Galaxy tools. The repository name must be a valid Posix disk file name, and when migrating the tools from the old tool archive-based tool shed to the new repository-based tool shed, the optimal choice for naming the repositories was to use a morphed version of the tool id. By "morphed" I mean that the tool id strings were lower-cased, and blank spaces were translated to underscore characters.

I would suggest using three columns / text boxes: ID, Name, Description e.g. based on the current XML file for this tool of mine,

ID: seq_filter_by_id Name: Filter sequences by ID Description: from a tabular file

Again, this assumes that every repository include 1 and only 1 Galaxy tool, which is an incorrect assumption. When browsing repositories, the list of repositories includes the name, synopsis and change log tip (version) of the repository. It does not display any information that may be included in any of the contained repository files. This may change in the future when I get further down the path of completing the repository metadata implementation, but no guarantee.

I have previously commented on the problem with showing the "description" on its own without the context of the tool name as displayed in Galaxy:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html

and:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html

One idea would be to show just the name in the left hand pane of Galaxy, with the description as a tool tip AND show this at the top of the tool main page in the central panel. This would encourage tool authors to write this field as a self contained synopsis, and make the left hand panel less text heavy.

This may be considered for the Galaxy instance (the decision is in the hands of others), but would probably not work in the tool shed. Again, we'll see what we can improve as I make progress on the repository metadata implementation.

Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu