diff --git a/q2_boots/plugin_setup.py b/q2_boots/plugin_setup.py index b3feec5..d02d9c1 100644 --- a/q2_boots/plugin_setup.py +++ b/q2_boots/plugin_setup.py @@ -7,8 +7,7 @@ # ---------------------------------------------------------------------------- from qiime2.plugin import (Plugin, Int, Range, Collection, - Citations, Str, Choices, Bool, Float, - Metadata, Visualization) + Citations, Str, Choices, Bool, Float) from q2_types.feature_table import ( FeatureTable, Frequency, RelativeFrequency, PresenceAbsence @@ -20,7 +19,6 @@ from q2_diversity_lib.alpha import METRICS as alpha_metrics from q2_diversity_lib.beta import METRICS as beta_metrics from q2_types.distance_matrix import DistanceMatrix -from q2_types.ordination import PCoAResults import q2_boots @@ -252,35 +250,35 @@ description='Average of a Collection of Distance Matrices' ) -plugin.pipelines.register_function( - function=q2_boots.core_metrics, - inputs={ - 'table': FeatureTable[Frequency | RelativeFrequency | - PresenceAbsence], - 'phylogeny': Phylogeny[Rooted], - }, - parameters={ - 'metadata': Metadata, - 'n_jobs': Int % Range(1, None), - 'n': Int % Range(1, None), - 'sampling_depth': Int % Range(1, None), - 'alpha_method': Str % Choices('mean', 'median'), - 'beta_method': Str % Choices('non-metric-mean', - 'non-metric-median', - 'medoid'), - 'with_replacement': Bool, - 'random_seed': Int - }, - outputs=[ - ('rarefied_table', Collection[FeatureTable[Frequency]]), - ('alpha_diversity', Collection[SampleData[AlphaDiversity]]), - ('distance_matrices', Collection[DistanceMatrix]), - ('pcoas', Collection[PCoAResults]), - ('visualizations', Collection[Visualization]), - ], - output_descriptions={ - - }, - name='Core Metrics', - description='Bootstrapped Core Metrics' -) +# plugin.pipelines.register_function( +# function=q2_boots.core_metrics, +# inputs={ +# 'table': FeatureTable[Frequency | RelativeFrequency | +# PresenceAbsence], +# 'phylogeny': Phylogeny[Rooted], +# }, +# parameters={ +# 'metadata': Metadata, +# 'n_jobs': Int % Range(1, None), +# 'n': Int % Range(1, None), +# 'sampling_depth': Int % Range(1, None), +# 'alpha_method': Str % Choices('mean', 'median'), +# 'beta_method': Str % Choices('non-metric-mean', +# 'non-metric-median', +# 'medoid'), +# 'with_replacement': Bool, +# 'random_seed': Int +# }, +# outputs=[ +# ('rarefied_table', Collection[FeatureTable[Frequency]]), +# ('alpha_diversity', Collection[SampleData[AlphaDiversity]]), +# ('distance_matrices', Collection[DistanceMatrix]), +# ('pcoas', Collection[PCoAResults]), +# ('visualizations', Collection[Visualization]), +# ], +# output_descriptions={ +# +# }, +# name='Core Metrics', +# description='Bootstrapped Core Metrics' +# )