Qiime tools import command, is import a plugin?

[jessicalmetcalf (Jessica Metcalf)]

Hi, I was trying to find info about import options on qiime2.org, but can’t find a plugin named “import” anywhere. Where is the info located in the qiime 2 documentation (e.g. when I type “qiime tools import --help”, I can find some info, where is this on the website?). Where are all the options for “–type” listed? Thanks!

[colinbrislawn (Colin J Brislawn)]

Hello Jessica,

Does this page help with importing?
https://docs.qiime2.org/2017.12/tutorials/importing/?highlight=import

Yeah, the names have changed (“scripts” -> “plugins”) and the URL keeps changing with every monthly release and I think that confuses Google.

All the plugins are here, but neither ‘tools’ or ‘import’ is on this page.
https://docs.qiime2.org/2017.12/plugins/available/

Colin

[jairideout (Jai Ram Rideout)]

Hi @jessicalmetcalf! To add to @colinbrislawn's reply:

All of the commands available under qiime tools, qiime dev, and qiime info are built-in commands provided by the CLI, and aren't QIIME 2 plugins (that's why you're not seeing them listed on the Available Plugins page). As @colinbrislawn noted, the best place to learn about importing is the Importing tutorial. That page doesn't list all semantic types and data formats (we included the most common ones for now). We're actively working to have more complete documentation on importing soon (likely within the next couple of releases). We'll follow up here when that's available!

@jessicalmetcalf

Where are all the options for “–type” listed?

There will more complete documentation on this in the future (see my note above), but to see a complete list of importable semantic types and data formats you can use the --show-importable-types and --show-importable-formats options, which simply print that info and exit:

If you have any questions about specific types or formats, feel free to create a new forum topic. Thanks!