Peter, this may be the Trello card you were thinking of.

https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois

Greg Von Kuster

On May 27, 2014, at 1:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

> Hi Eric,
>
> I was sure there was a Trello card for this, but I can't find it right now...
>
> I've pushed this idea on the mailing list before, and in person at
> the Galaxy Community Conference too. See also these threads:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html
>
> Are you familiar enough with the area of semantic web/linked
> data to know what would be the best XML based markup to
> use for embedding the citations?
>
> i.e. We should not reinvent the wheel here ;)
>
> Peter
>
>
> On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org> wrote:
>> Eric, I'm very much in favor of this feature, and particularly the
>> idea of generating a list of citations from a history or workflow. I
>> imagine the only thing to quibble about will be the syntax. There are
>> already some efforts to represent bibtex in xml (e.g.
>> https://github.com/Zearin/BibTeXML), however they have always struck
>> me as overly verbose.
>>
>> -- jt
>>
>>
>> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru> wrote:
>>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA1
>>>
>>> I'd want to open up discussion on a feature I'd like to see. I'll try
>>> and implement it if I can find time this summer. I didn't see a trello
>>> card for anything like this yet, but please feel free to direct me there
>>> if I missed it.
>>>
>>>
>>> I'd like to see citations as a part of every tool.
>>>
>>> This would happen in the form of a <citation> block in the XML, which
>>> would contain sub-elements with text. These sub-elements could be based
>>> off of BibTeX, since they have existing specs for citing things:
>>> https://en.wikipedia.org/wiki/BibTeX
>>>
>>> These citations would then be accessible in the HTML generated tool
>>> pages, or via a View/Download button somewhere on the tool page. By
>>> storing as an XML tree, we could render these citations as BibTeX
>>> entries for the LaTeX users, and I believe there are ways to convert
>>> BibTeX to EndNote XML and so on.
>>>
>>> This could be extended for use in workflows so that when you run
>>> workflows, somehow a list of citations for all tools used could be
>>> generated.
>>>
>>> Anyone have thoughts or opinions on this?
>>>
>>>
>>>
>>>
>>> Using the example bibtex entry from the wikipedia page:
>>>
>>> @Book{abramowitz+stegun,
>>> author    = "Milton {Abramowitz} and Irene A. {Stegun}",
>>> title     = "Handbook of Mathematical Functions with
>>>              Formulas, Graphs, and Mathematical Tables",
>>> publisher = "Dover",
>>> year      =  1964,
>>> address   = "New York",
>>> edition   = "ninth Dover printing, tenth GPO printing"
>>> }
>>>
>>> I imagine it'd look like the following in a real-life tool:
>>>
>>> <tool>
>>>  ...
>>>  <citation type="book">
>>>    <author>Milton Abramowitz and Irene A. Stegun"</author>
>>>    <title>Handbook of Mathematical Functions with Formulas, Graphs, and
>>> Mathematical Tables</title>
>>>    <publisher>Dover</publisher>
>>>    <year>1964</year>
>>>    <address>New York</address>
>>>    <edition>ninth Dover printing, tenth GPO printing</edition>
>>>  </citation>
>>> </tool>
>>>
>>>
>>> Cheers,
>>> Eric
>>> - --
>>> Eric Rasche
>>> Programmer II
>>> Center for Phage Technology
>>> Texas A&M University
>>> College Station, TX 77843
>>> 404-692-2048
>>> esr@tamu.edu
>>> rasche.eric@yandex.ru
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