galaxy pasteur tool name

[hansioan]

Names of galaxy pasteur tools end in -IP, I think we should changed that to be (IP)
example: trimmomatic-IP becomes trimmomatic (IP)

@joncison you agree?

[joncison]

According to naming patterns (http://biotools.readthedocs.io/en/latest/curators_guide.html#id18) that's right but if I recall right, I didn't bother renaming (in the spreadsheet from hell) tools whose descriptions are generated automatically, such as for Galaxy Pasteur. Probably better to update regate (the tooling used for this), cc @hmenager to advise!

[hansioan]

@joncison to take this as a final stage of refactoring for "canonical" entries.

[joncison]

As discussed with @hmenager and @hansioan, I will go through these "*-IP" entries systematically, identifying ...

... entries where an independent tool exists, should be refactored into "canonical" entries (i.e. ):

1. retain existing homepage as <link><url>...</url><type>Service</type></link>
2. change homepage to tool homepage (not Galaxy)
3. change both name and ID, e.g. "breseq-IP" -> "breseq"

entries for which an independent tool does not exist

1. change name e.g. "breseq-IP" -> "breseq (IP)"

(this will need a revision to biotoolsSchema, see bio-tools/biotoolsSchema#129)

[joncison]

@hmenager - I took a look at this, but multiple things cropped up:

• there are some tools in the IP Galaxy that we don't have
• some tools we do have, but which are obsolete
• some of IP Galaxy services wrap tools belonging to suites, e.g. of SAM tools. It would be good to have these - but ideally we'd need a way to formally relate such entries in bio.tools (see Modelling tool relations and versions (placeholder discussion) biotoolsSchema#106)
• I suspect some services wrap individual functions / modes of operations of tools - need to investigate this more / decide what to do
• in cases where we want to convert an entry to describe the "canonical" tool, we want to preserve the link to IP Galaxy, which needs a new schema element (see Add "Service" to <link><type> enum biotoolsSchema#129)

Doing this is too much for this year, so I propose we get together with @hansioan next year, and dedicate a few days to this, and get it right. Is that OK?

[joncison]

@hmenager @hansioan can we take a quick skype this morning to discuss briefly ... Hans and I need to understand, of the tools imported from Galaxy pasteur (where the descriptions are awesome, by the way!), what tools exist only in that instance (and so can keep their name/IDs) and what tools exist independently (where we'd need to merge into / create the "canonical" entries with appropriate names and IDs)

[joncison]

update from call with @hmenager & @hansioan we now have:
https://docs.google.com/spreadsheets/d/13sJxbfzG1rbfoqiKo_ilB4ZEKd0EmhDUoz55iYFDpHM/edit#gid=0

Actions:

• Herve to complete spreadsheet and hand over to Hans & I
• rename tools & IDs dropping the "-IP" suffix
• preserve existing homepage as link
• hotfix link->type enum extension for "Galaxy service" (see Add "Service" to <link><type> enum biotoolsSchema#129) (using this for links)
• assign tools in suites (or "functional units" in packages) to a collection annotation (to be later refactored using formalised relationships)
• ensure we have corresponding entries for all the suites / packages bundled in Galaxy IP, e.g. that we have a bedtools entry (also annotating this to the corresponding collection)

[joncison]

all now done @hmenager

[joncison]

done