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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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jbrowse: add 'product' to style:{description} list #795

Closed tseemann closed 8 years ago

tseemann commented 8 years ago

Microbial genomics use the /product field for protein names. Please add it to the default tags to label features please, as below:

  "style": {
    "label": "name,id",
    "description": "product,note,description",
}
hexylena commented 8 years ago

And us viral people do as well :) However, when I built the tool, I tried to wrap it fairly closely to the default JBrowse configuration. Upstream had chosen that as their default and given that it was exposed as a configurable option, I had no strong rationale from deviating from their default. I'll see if I can add this to the next round of updates, but I don't wish to make this tool any more specific to one group than another (w/r/t default configuration).

https://github.com/galaxyproject/tools-iuc/blob/master/tools/jbrowse/macros.xml#L221

tseemann commented 8 years ago

My argument would be that product is the official INSDC (Genbank etc) field for the protein name, which is what you want shown in a CDS feature.

http://www.insdc.org/documents/feature_table.html

description is not official GFF or anything?

Maybe I need to argue with Ian Holmes (@ihh) on this one :)

hexylena commented 8 years ago

which is what you want shown in a CDS feature.

Oh, yes, definitely. I come from a ... very limited world view (only viral data), and was trying not to encode any of my prior assumptions about data/field usage. Adding product should be a relatively low impact change.

description is not official GFF or anything?

Indeed, that does make it an odd default.

nsoranzo commented 8 years ago

Should be fixed by #851.