q2-types

This QIIME 2 plugin defines semantic types and transformers supporting microbiome analysis.

version: 2025.7.0.dev0

website: https://github.com/qiime2/q2-types

user support:

Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Artifact Classes¶

Formats¶

types partition-sample-data-mags¶

Partition a SampleData[MAGs] artifact into smaller artifacts containing subsets of the MAGs

Inputs¶

mags: SampleData[MAGs]

The MAGs to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The number of partitions to split the MAGs into. Defaults to partitioning into individual MAGs.[optional]

Outputs¶

partitioned_mags: Collection[SampleData[MAGs]]

<no description>[required]

types partition-samples-single¶

Partition demultiplexed single end or joined sequences into individual samples or the number of partitions specified.

Inputs¶

demux: SampleData[SequencesWithQuality¹ | JoinedSequencesWithQuality²]

The demultiplexed sequences to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The number of partitions to split the demultiplexed sequences into. Defaults to partitioning into individual samples.[optional]

Outputs¶

partitioned_demux: Collection[SampleData[SequencesWithQuality¹ | JoinedSequencesWithQuality²]]

The partitioned demultiplexed sequences.[required]

types partition-samples-paired¶

Partition demultiplexed paired end sequences into individual samples or the number of partitions specified.

Inputs¶

demux: SampleData[PairedEndSequencesWithQuality]

The demultiplexed sequences to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The number of partitions to split the demultiplexed sequences into. Defaults to partitioning into individual samples.[optional]

Outputs¶

partitioned_demux: Collection[SampleData[PairedEndSequencesWithQuality]]

The partitioned demultiplexed sequences.[required]

types partition-orthologs¶

Partition a SampleData[BLAST6] artifact into smaller artifacts containing subsets of the BLAST6 reports.

Inputs¶

orthologs: SampleData[Orthologs]

The orthologs to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The number of partitions to split the MAGs into. Defaults to partitioning into individual MAGs.[optional]

Outputs¶

partitioned_orthologs: Collection[SampleData[Orthologs]]

<no description>[required]

types collate-sample-data-mags¶

Takes a collection of SampleData[MAGs]'s and collates them into a single artifact.

Inputs¶

mags: List[SampleData[MAGs]]

A collection of MAGs to be collated.[required]

Outputs¶

collated_mags: SampleData[MAGs]

<no description>[required]

types partition-feature-data-mags¶

Partition a FeatureData[MAG] artifact into smaller artifacts containing subsets of the MAGs

Inputs¶

mags: FeatureData[MAG]

MAGs to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The number of partitions to split the MAGs into. Defaults to partitioning into individual MAGs.[optional]

Outputs¶

partitioned_mags: Collection[FeatureData[MAG]]

<no description>[required]

types collate-feature-data-mags¶

Takes a collection of FeatureData[MAG]'s and collates them into a single artifact.

Inputs¶

mags: List[FeatureData[MAG]]

A collection of MAGs to be collated.[required]

Outputs¶

collated_mags: FeatureData[MAG]

<no description>[required]

types collate-orthologs¶

Takes a collection SampleData[BLAST6] artifacts and collates them into a single artifact.

Inputs¶

orthologs: List[SampleData[Orthologs]]

Orthologs to collate[required]

Outputs¶

collated_orthologs: SampleData[Orthologs]

<no description>[required]

types collate-ortholog-annotations¶

Takes a collection of GenomeData[NOG]'s and collates them into a single artifact.

Inputs¶

ortholog_annotations: List[GenomeData[NOG]]

Collection of ortholog annotations.[required]

Outputs¶

collated_annotations: GenomeData[NOG]

Collated ortholog annotations.[required]

types collate-loci¶

Takes a collection of GenomeData[Loci]'s and collates them into a single artifact.

Inputs¶

loci: List[GenomeData[Loci]]

A collection of loci to be collated.[required]

Outputs¶

collated_loci: GenomeData[Loci]

<no description>[required]

types collate-kraken2-reports¶

Inputs¶

kraken2_reports: List[SampleData[Kraken2Report % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Report % Properties('contigs', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'contigs')] | SampleData[Kraken2Report % Properties('reads')] | SampleData[Kraken2Report % Properties('contigs')] | SampleData[Kraken2Report % Properties('mags')] | FeatureData[Kraken2Report % Properties('mags')]]

The kraken2 reports to collate.[required]

Outputs¶

collated_kraken2_reports: SampleData[Kraken2Report % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Report % Properties('contigs', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'contigs')] | SampleData[Kraken2Report % Properties('reads')] | SampleData[Kraken2Report % Properties('contigs')] | SampleData[Kraken2Report % Properties('mags')] | FeatureData[Kraken2Report % Properties('mags')]

The collated kraken2 reports.[required]

types collate-kraken2-outputs¶

Inputs¶

kraken2_outputs: List[SampleData[Kraken2Output % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Output % Properties('contigs', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'contigs')] | SampleData[Kraken2Output % Properties('reads')] | SampleData[Kraken2Output % Properties('contigs')] | SampleData[Kraken2Output % Properties('mags')] | FeatureData[Kraken2Output % Properties('mags')]]

The kraken2 outputs to collate.[required]

Outputs¶

collated_kraken2_outputs: SampleData[Kraken2Output % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Output % Properties('contigs', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'contigs')] | SampleData[Kraken2Output % Properties('reads')] | SampleData[Kraken2Output % Properties('contigs')] | SampleData[Kraken2Output % Properties('mags')] | FeatureData[Kraken2Output % Properties('mags')]

The collated kraken2 outputs.[required]

types partition-kraken2-reports¶

Inputs¶

reports: SampleData[Kraken2Report % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Report % Properties('contigs', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'contigs')] | SampleData[Kraken2Report % Properties('reads')] | SampleData[Kraken2Report % Properties('contigs')] | SampleData[Kraken2Report % Properties('mags')] | FeatureData[Kraken2Report % Properties('mags')]

The kraken2 reports to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The desired number of partitions. Defaults to one partition per sample.[optional]

Outputs¶

partitioned_reports: Collection[SampleData[Kraken2Report % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Report % Properties('contigs', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'mags')] | SampleData[Kraken2Report % Properties('reads', 'contigs')] | SampleData[Kraken2Report % Properties('reads')] | SampleData[Kraken2Report % Properties('contigs')] | SampleData[Kraken2Report % Properties('mags')] | FeatureData[Kraken2Report % Properties('mags')]]

The partitioned kraken2 reports.[required]

types partition-kraken2-outputs¶

Inputs¶

outputs: SampleData[Kraken2Output % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Output % Properties('contigs', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'contigs')] | SampleData[Kraken2Output % Properties('reads')] | SampleData[Kraken2Output % Properties('contigs')] | SampleData[Kraken2Output % Properties('mags')] | FeatureData[Kraken2Output % Properties('mags')]

The kraken2 outputs to partition.[required]

Parameters¶

num_partitions: Int % Range(1, None)

The desired number of partitions. Defaults to one partition per sample.[optional]

Outputs¶

partitioned_outputs: Collection[SampleData[Kraken2Output % Properties('reads', 'contigs', 'mags')] | SampleData[Kraken2Output % Properties('contigs', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'mags')] | SampleData[Kraken2Output % Properties('reads', 'contigs')] | SampleData[Kraken2Output % Properties('reads')] | SampleData[Kraken2Output % Properties('contigs')] | SampleData[Kraken2Output % Properties('mags')] | FeatureData[Kraken2Output % Properties('mags')]]

The partitioned kraken2 outputs.[required]