from q2_types.tree import Phylogeny, Rooted
from q2_types.ordination import PCoAResults
plugin = Plugin(
name='diversity',
version=q2_diversity.__version__,
website='https://github.com/qiime2/q2-diversity',
package='q2_diversity'
)
plugin.methods.register_function(
function=q2_diversity.beta_phylogenetic,
inputs={'table': FeatureTable[Frequency] % Properties('uniform-sampling'),
'phylogeny': Phylogeny[Rooted]},
parameters={'metric': Str % Choices(beta.phylogenetic_metrics())},
outputs=[('distance_matrix', DistanceMatrix % Properties('phylogenetic'))],
input_descriptions={
'table': ('The feature table containing the samples over which beta '
'diversity should be computed.'),
'phylogeny': ('Phylogenetic tree containing tip identifiers that '
'correspond to the feature identifiers in the table. '
'This tree can contain tip ids that are not present in '
'the table, but all feature ids in the table must be '
'present in this tree.')
},
parameter_descriptions={
'metric': 'The beta diversity metric to be computed.'
},
output_descriptions={'distance_matrix': 'The resulting distance matrix.'},
name='Beta diversity (phylogenetic)',
package='q2_diversity',
description=('This QIIME 2 plugin supports metrics for calculating '
'and exploring community alpha and beta diversity through '
'statistics and visualizations in the context of sample '
'metadata.'),
short_description='Plugin for exploring community diversity.',
)
plugin.methods.register_function(
function=q2_diversity.beta_phylogenetic,
inputs={
'table': FeatureTable[Frequency],
'phylogeny': Phylogeny[Rooted]
},
parameters={
'metric': Str % Choices(beta.phylogenetic_metrics()),
'n_jobs': Int % Range(1, None)
},
outputs=[('distance_matrix', DistanceMatrix % Properties('phylogenetic'))],
input_descriptions={
'table': ('The feature table containing the samples over which beta '
'diversity should be computed.'),
'phylogeny': ('Phylogenetic tree containing tip identifiers that '
'correspond to the feature identifiers in the table. '
'This tree can contain tip ids that are not present in '
'the table, but all feature ids in the table must be '
'present in this tree.')
},
parameter_descriptions={
'metric': 'The beta diversity metric to be computed.',
'n_jobs':
from q2_types.tree import Phylogeny, Rooted
from q2_types.ordination import PCoAResults
plugin = Plugin(
name='diversity',
version=q2_diversity.__version__,
website='https://github.com/qiime2/q2-diversity',
package='q2_diversity'
)
plugin.methods.register_function(
function=q2_diversity.beta_phylogenetic,
inputs={'table': FeatureTable[Frequency] % Properties('uniform-sampling'),
'phylogeny': Phylogeny[Rooted]},
parameters={'metric': Str % Choices(beta.phylogenetic_metrics())},
outputs=[('distance_matrix', DistanceMatrix % Properties('phylogenetic'))],
input_descriptions={
'table': ('The feature table containing the samples over which beta '
'diversity should be computed.'),
'phylogeny': ('Phylogenetic tree containing tip identifiers that '
'correspond to the feature identifiers in the table. '
'This tree can contain tip ids that are not present in '
'the table, but all feature ids in the table must be '
'present in this tree.')
},
parameter_descriptions={
'metric': 'The beta diversity metric to be computed.'
},
output_descriptions={'distance_matrix': 'The resulting distance matrix.'},
name='Beta diversity (phylogenetic)',
