QIIME Importing Options?

[Micro_Biologist (Jono Warren)]

Hello,

pretty easy Qu for the devs!

Is there any information about the parameters available to use when importing data into qiime?

I tried looking in the plugins page and found nothing.

Thanks, Jono

[ebolyen (Evan Bolyen)]

Hey @Micro_Biologist,

You can use:

qiime tools import --show-importable-formats

and

qiime tools import --show-importable-types

Documentation on what those mean exactly doesn't really exist yet . If you are willing to scrounge around q2-types you can read what the definitions of these formats are by their source-code though.

[Micro_Biologist (Jono Warren)]

Thanks for the information, however I more meant what options can we pass to qiime tools import, such as the amount of cores/threads to use? Can we use the --verbose command to show more information?

[thermokarst]

Hi @Micro_Biologist! Every q2cli command supports the --help flag for learning more about available options:

$  qiime tools import --help
Usage: qiime tools import [OPTIONS]

  Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/
  for usage examples and details on the file types and associated semantic
  types that can be imported.

Options:
  --type TEXT                The semantic type of the artifact that will be
                             created upon importing. Use --show-importable-
                             types to see what importable semantic types are
                             available in the current deployment.  [required]
  --input-path PATH          Path to file or directory that should be
                             imported.  [required]
  --output-path PATH         Path where output artifact should be written.
                             [required]
  --source-format TEXT       The format of the data to be imported. If not
                             provided, data must be in the format expected by
                             the semantic type provided via --type.
  --show-importable-types    Show the semantic types that can be supplied to
                             --type to import data into an artifact.
  --show-importable-formats  Show formats that can be supplied to --source-
                             format to import data into an artifact.
  --help                     Show this message and exit.

As far as specifying the number of cores or threads for importing, we don't support that at present. Hope that helps!