qiime2 taxa collapse (version 2024.5.0+q2galaxy.2024.5.0)

table: FeatureTable[Frequency]:

[required] Feature table to be collapsed.

taxonomy: FeatureData[Taxonomy]:

[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.

level: Int:

[required] The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation.

QIIME 2: taxa collapse

Collapse features by their taxonomy at the specified level

Outputs:

collapsed_table.qza:
	The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels.

Description:

Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.

Examples:

collapse

Using the qiime2 taxa collapse tool:

Set "table" to #: table.qza
Set "taxonomy" to #: taxonomy.qza
Set "level" to 6
Press the Execute button.

Once completed, for the new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name	"Name" to set (be sure to press `Save`)
`#: qiime2 taxa collapse [...] : collapsed_table.qza`	`collapsed-table-l6.qza`