On Mon, Aug 4, 2014 at 4:28 PM, Eric Rasche <rasche.e...@yandex.ru> wrote:
> Hi Peter,
> On 08/04/2014 09:25 AM, Peter Cock wrote:
>> Hi Mert,
>> Most of the Galaxy tools dealing with tables of data use "tabular"
>> format (tab separated variables), not csv (comma separated
>> variables). CVS is a horrible horrible mess of formats, see e.g.
>> http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/
> This annoyed me when I was first starting out with galaxy, I really wish
> it'd be labelled TSV. The labels all read "CSV" so I gave galaxy "CSV"
> data and galaxy didn't like it, much to my confusion.

Which labels say "CSV" at the moment?

(And yes, I would also have preferred "tsv" to "tabular" as the datatype
name in Galaxy, that way it would match the typical file extension).

> Also, most (biologists) I work with use the term CSV very generically
> without regard to the differences between the two.

I've seen that too - but people saying CSV when they mean TSV
will unavoidable cause confusion.

>> Also beware that anything other than MS Excel could be
>> confused by quirks in the Excel format, e.g. multiple ways
>> to record dates: http://support.microsoft.com/kb/180162
>> I would personally save each tab of the Excel sheet as tab
>> separated data, and import those into Galaxy.
> Would it not make sense to have an XLS <-> TSV datatype converter? I'm
> sure many biologists would appreciate being able to use the in-galaxy
> version as opposed to having to open+re-save all of their data.

It makes sense to me to offer a tool mapping one Excel sheet to
multiple tabular output files (one per sheet). How best to write
this will depend on the platform and available dependencies
(e.g. some of the R converters for this are Windows only IIRC).

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