from qiime2.plugin import (Str, Int, Choices, MetadataCategory, Plugin)
from q2_types.feature_table import FeatureTable, Frequency, Composition
import q2_composition
_citation_text = ("Analysis of composition of microbiomes: a novel method for "
"studying microbial composition.\nMandal S, Van Treuren W, "
"White RA, Eggesbø M, Knight R, Peddada SD.\n"
"Microb Ecol Health Dis. 2015 May 29;26:27663. doi: "
"10.3402/mehd.v26.27663.")
plugin = Plugin(name='composition',
version=q2_composition.__version__,
website='https://github.com/qiime2/q2-composition',
citation_text=_citation_text,
package='q2_composition',
description=('This QIIME 2 plugin supports methods for '
'compositional data analysis.'),
short_description='Plugin for compositional data analysis.')
plugin.methods.register_function(
function=q2_composition.add_pseudocount,
inputs={'table': FeatureTable[Frequency]},
parameters={'pseudocount': Int},
outputs=[('composition_table', FeatureTable[Composition])],
input_descriptions={
'table': 'The feature table to which pseudocounts should be added.'
},
parameter_descriptions={
'pseudocount': 'The value to add to all counts in the feature table.'
},
typical_pipeline_simple,
typical_pipeline_complex,
comments_only,
identity_with_metadata_simple,
identity_with_metadata_merging,
identity_with_metadata_column_get_mdc,
variadic_input_simple,
optional_inputs,
)
citations = Citations.load('citations.bib', package='qiime2.core.testing')
dummy_plugin = Plugin(
name='dummy-plugin',
description='Description of dummy plugin.',
short_description='Dummy plugin for testing.',
version='0.0.0-dev',
website='https://github.com/qiime2/qiime2',
package='qiime2.core.testing',
user_support_text='For help, see https://qiime2.org',
citations=[citations['unger1998does'], citations['berry1997flying']])
import_module('qiime2.core.testing.transformer')
# Register semantic types
dummy_plugin.register_semantic_types(IntSequence1, IntSequence2, IntSequence3,
Mapping, FourInts, Kennel, Dog, Cat,
SingleInt, C1, C2, C3, Foo, Bar, Baz)
# Register formats
dummy_plugin.register_formats(IntSequenceFormatV2, MappingFormat,
IntSequenceV2DirectoryFormat,
from ._prune_hierarchy import prune_hierarchy
from ._classyfire import get_classyfire_taxonomy
from ._semantics import (MassSpectrometryFeatures, MGFDirFmt,
SiriusFolder, SiriusDirFmt,
ZodiacFolder, ZodiacDirFmt,
CSIFolder, CSIDirFmt,
FeatureData, TSVMoleculesFormat, Molecules)
from qiime2.plugin import Plugin, Str, Range, Choices, Float, Int, Bool, List
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.tree import Phylogeny, Rooted
plugin = Plugin(
name='qemistree',
version=q2_qemistree.__version__,
website='https://github.com/biocore/q2-qemistree',
package='q2_qemistree',
description='Hierarchical orderings for mass spectrometry data',
short_description='Plugin for exploring chemical diversity.',
)
# type registration
plugin.register_views(MGFDirFmt)
plugin.register_semantic_types(MassSpectrometryFeatures)
plugin.register_semantic_type_to_format(MassSpectrometryFeatures,
artifact_format=MGFDirFmt)
plugin.register_views(SiriusDirFmt)
plugin.register_semantic_types(SiriusFolder)
plugin.register_semantic_type_to_format(SiriusFolder,
artifact_format=SiriusDirFmt)
from qiime2.plugin import (Plugin, Str, Properties, MetadataCategory, Choices,
Metadata, Int)
import q2_diversity
from q2_diversity import _alpha as alpha
from q2_diversity import _beta as beta
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.distance_matrix import DistanceMatrix
from q2_types.sample_data import AlphaDiversity, SampleData
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 '
from q2_types.feature_data import FeatureData, AlignedSequence
from q2_types.tree import Phylogeny
import q2_beast
from q2_beast.methods import (site_heterogeneous_hky, merge_chains,
maximum_clade_credibility, gtr_single_partition)
from q2_beast.visualizations import traceplot
from q2_beast.types import Chain, BEAST, MCC
from q2_beast.formats import (PosteriorLogFormat, NexusFormat,
BEASTControlFileFormat, BEASTOpsFileFormat,
BEASTPosteriorDirFmt, NexusDirFmt)
plugin = Plugin(name='beast',
website='',
package='q2_beast',
version=q2_beast.__version__,
description='',
short_description='')
plugin.register_formats(PosteriorLogFormat, NexusFormat,
BEASTControlFileFormat, BEASTOpsFileFormat,
BEASTPosteriorDirFmt, NexusDirFmt)
plugin.register_semantic_types(Chain, BEAST, MCC)
plugin.register_semantic_type_to_format(Chain[BEAST],
artifact_format=BEASTPosteriorDirFmt)
plugin.register_semantic_type_to_format(Phylogeny[MCC],
artifact_format=NexusDirFmt)
importlib.import_module('q2_beast.transformers')
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import q2_emperor
from ._plot import plot
from qiime2.plugin import Plugin, Metadata, Str
from q2_types.ordination import PCoAResults
plugin = Plugin(
name='emperor',
version=q2_emperor.__version__,
website='http://emperor.microbio.me',
package='q2_emperor',
citation_text=('EMPeror: a tool for visualizing high-'
'throughput microbial community data.\nVazquez-Baeza Y, '
'Pirrung M, Gonzalez A, Knight R.\nGigascience. '
'2013 Nov 26;2(1):16.'),
description=('This QIIME 2 plugin wraps Emperor and '
'supports interactive visualization of ordination '
'plots.'),
short_description='Plugin for ordination plotting with Emperor.')
plugin.visualizers.register_function(
function=plot,
inputs={'pcoa': PCoAResults},
parameters={
'metadata': Metadata,
'custom_axis': Str
},
input_descriptions={
JoinedSequencesWithQuality)
import q2_demux
from ._type import (RawSequences, EMPSingleEndSequences, EMPPairedEndSequences,
ErrorCorrectionDetails)
from ._format import (EMPMultiplexedDirFmt, ErrorCorrectionDetailsDirFmt,
EMPSingleEndDirFmt, EMPSingleEndCasavaDirFmt,
EMPPairedEndDirFmt, EMPPairedEndCasavaDirFmt)
citations = Citations.load('citations.bib', package='q2_demux')
plugin = Plugin(
name='demux',
version=q2_demux.__version__,
website='https://github.com/qiime2/q2-demux',
package='q2_demux',
description=('This QIIME 2 plugin supports demultiplexing of '
'single-end and paired-end sequence reads and '
'visualization of sequence quality information.'),
short_description='Plugin for demultiplexing & viewing sequence quality.'
)
plugin.register_semantic_types(
RawSequences, EMPSingleEndSequences, EMPPairedEndSequences,
ErrorCorrectionDetails)
plugin.register_formats(EMPMultiplexedDirFmt, ErrorCorrectionDetailsDirFmt,
EMPSingleEndDirFmt, EMPSingleEndCasavaDirFmt,
EMPPairedEndDirFmt, EMPPairedEndCasavaDirFmt)
# TODO: remove when aliasing exists
plugin.register_semantic_type_to_format(
Citations, TypeMatch, TypeMap)
import q2_feature_table
from q2_types.feature_table import (FeatureTable, Frequency, RelativeFrequency,
PresenceAbsence, Composition)
from q2_types.feature_data import (FeatureData, Sequence, Taxonomy,
AlignedSequence)
from .examples import (feature_table_merge_example,
feature_table_merge_three_tables_example)
citations = Citations.load('citations.bib', package='q2_feature_table')
plugin = Plugin(
name='feature-table',
version=q2_feature_table.__version__,
website='https://github.com/qiime2/q2-feature-table',
package='q2_feature_table',
short_description=('Plugin for working with sample by feature tables.'),
description=('This is a QIIME 2 plugin supporting operations on sample '
'by feature tables, such as filtering, merging, and '
'transforming tables.'))
plugin.methods.register_function(
function=q2_feature_table.rarefy,
inputs={'table': FeatureTable[Frequency]},
parameters={
'sampling_depth': Int % Range(1, None),
'with_replacement': Bool
},
outputs=[('rarefied_table', FeatureTable[Frequency])],
input_descriptions={'table': 'The feature table to be rarefied.'},
parameter_descriptions={
# ----------------------------------------------------------------------------
# Copyright (c) 2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import q2_cutadapt
from qiime2.plugin import Plugin
plugin = Plugin(
name='cutadapt',
version=q2_cutadapt.__version__,
website='https://github.com/qiime2/q2-cutadapt',
package='q2_cutadapt',
description='This QIIME 2 plugin supports removing adapters, primers, '
'and other unwanted sequences from sequence data.',
short_description='Plugin for removing unwanted sequences from sequence '
'data.',
)
import qiime2
from qiime2.plugin import Plugin, Metadata, Int, Range
from q2_types.feature_data import FeatureData
import q2_covid
from q2_covid.common import (IDSelectionDirFmt, IDSelection, Selection,
IDMetadataFormat, UNIXListFormat)
from q2_covid.subsample_random import subsample_random
plugin = Plugin(
name='covid',
website='https://github.com/caporaso-lab/q2-covid',
package='q2_covid',
version=q2_covid.__version__,
description='Tools for genomic epidemiology focused on the SARS-CoV-2'
' virus.',
short_description='Tools for genomic epidemiology.'
)
plugin.register_formats(IDSelectionDirFmt)
plugin.register_semantic_types(Selection)
plugin.register_semantic_type_to_format(FeatureData[Selection],
artifact_format=IDSelectionDirFmt)
@plugin.register_transformer
def _1(obj: IDSelection) -> IDSelectionDirFmt:
result = IDSelectionDirFmt()
inclusion = obj.inclusion
assert not inclusion.index.has_duplicates
from q2_types.distance_matrix import DistanceMatrix
from q2_types.tree import Phylogeny, Rooted
from ._format import (CoordinatesFormat, CoordinatesDirectoryFormat,
QuadTreeFormat, QuadTreeDirectoryFormat)
from ._type import (Coordinates, QuadTree)
from .stats import autocorr
from .qtrees import quadtree
citations = Citations.load('citations.bib', package='q2_coordinates')
plugin = Plugin(
name='coordinates',
version=q2_coordinates.__version__,
website="https://github.com/nbokulich/q2-coordinates",
package='q2_coordinates',
description=(
'This QIIME 2 plugin supports methods for geospatial analysis and map '
'building.'),
short_description=(
'Plugin for geospatial analysis and cartography.'),
)
base_parameters = {
'metadata': Metadata,
'latitude': Str,
'longitude': Str,
'missing_data': Str
}
base_parameter_descriptions = {
from q2_types.feature_data import FeatureData, Sequence
from q2_types.tree import Phylogeny, Rooted
import q2_picrust2
citations = Citations.load('citations.bib', package='q2_picrust2')
HSP_METHODS = ['mp', 'emp_prob', 'pic', 'scp', 'subtree_average']
PLACEMENT_TOOLS = ['epa-ng', 'sepp']
plugin = Plugin(
name='picrust2',
version="2021.11",
website='https://github.com/gavinmdouglas/q2-picrust2',
package='q2_picrust2',
description=(
'This QIIME 2 plugin wraps the default 16S PICRUSt2 pipeline to run '
'metagenome inference based on marker gene data. Currently '
'only unstratified output is supported.'),
short_description='Predicts gene families and pathways from 16S sequences.',
citations=[citations['Douglas2020NatureBiotech']])
plugin.methods.register_function(
function=q2_picrust2.full_pipeline,
inputs={
'table': FeatureTable[Frequency],
'seq': FeatureData[Sequence]
},
parameters={
'threads': Int % Range(1, None),
'hsp_method': Str % Choices(HSP_METHODS),
optional_artifacts_method, long_description_method,
docstring_order_method, variadic_input_method)
from .visualizer import (most_common_viz, mapping_viz, params_only_viz,
no_input_viz)
from .pipeline import (parameter_only_pipeline, typical_pipeline,
optional_artifact_pipeline, visualizer_only_pipeline,
pipelines_in_pipeline, pointless_pipeline,
failing_pipeline)
from ..cite import Citations
citations = Citations.load('citations.bib', package='qiime2.core.testing')
dummy_plugin = Plugin(
name='dummy-plugin',
description='Description of dummy plugin.',
short_description='Dummy plugin for testing.',
version='0.0.0-dev',
website='https://github.com/qiime2/qiime2',
package='qiime2.core.testing',
user_support_text='For help, see https://qiime2.org',
citations=[citations['unger1998does'], citations['berry1997flying']]
)
import_module('qiime2.core.testing.transformer')
# Register semantic types
dummy_plugin.register_semantic_types(IntSequence1, IntSequence2, Mapping,
FourInts, Kennel, Dog, Cat, SingleInt)
# Register formats
dummy_plugin.register_formats(
IntSequenceFormatV2, MappingFormat, IntSequenceV2DirectoryFormat,
MappingDirectoryFormat)
from qiime2.plugin import Plugin
import qiime2.plugin
import q2_cscs.q2_cscs
import biom
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.distance_matrix import DistanceMatrix
from q2_types.tree import Phylogeny, Rooted
from qiime2.plugin import Str, Choices, Properties, Metadata
plugin = Plugin(name='cscs',
version='0.0.1',
website='https://qiime2.org',
user_support_text='https://forum.qiime2.org',
package='q2_cscs')
plugin.methods.register_function(
function=q2_cscs.q2_cscs.cscs,
inputs={
'features': FeatureTable[Frequency],
},
parameters={
'css_edges': qiime2.plugin.Str,
'weighted': qiime2.plugin.Bool,
'normalization': qiime2.plugin.Bool,
'cosine_threshold':
qiime2.plugin.Float % qiime2.plugin.Range(0., None),
'cpus': qiime2.plugin.Int,
'chunk': qiime2.plugin.Int
},
outputs=[('distance_matrix', DistanceMatrix % Properties('phylogenetic'))],
input_descriptions={
from qiime2.plugin import (Str, Plugin, Choices, Range, Float, Int, Bool,
MetadataColumn, Categorical, Citations)
from q2_types.feature_data import FeatureData, Sequence, Taxonomy
from q2_types.feature_table import FeatureTable, RelativeFrequency
from .quality_control import (exclude_seqs, evaluate_composition,
evaluate_seqs, evaluate_taxonomy)
citations = Citations.load('citations.bib', package='q2_quality_control')
plugin = Plugin(
name='quality-control',
version=q2_quality_control.__version__,
website='https://github.com/qiime2/q2-quality-control',
package='q2_quality_control',
description=(
'This QIIME 2 plugin supports methods for assessing and controlling '
'the quality of feature and sequence data.'),
short_description=(
'Plugin for quality control of feature and sequence data.')
)
seq_inputs = {'query_sequences': FeatureData[Sequence],
'reference_sequences': FeatureData[Sequence]}
seq_inputs_descriptions = {
'query_sequences': 'Sequences to test for exclusion',
'reference_sequences': ('Reference sequences to align against feature '
'sequences')}
identity_with_optional_metadata_column,
params_only_method, no_input_method,
optional_artifacts_method, long_description_method,
variadic_input_method)
from .visualizer import (most_common_viz, mapping_viz, params_only_viz,
no_input_viz)
from .pipeline import (parameter_only_pipeline, typical_pipeline,
optional_artifact_pipeline, visualizer_only_pipeline,
pipelines_in_pipeline, pointless_pipeline,
failing_pipeline)
dummy_plugin = Plugin(
name='dummy-plugin',
description='Description of dummy plugin.',
short_description='Dummy plugin for testing.',
version='0.0.0-dev',
website='https://github.com/qiime2/qiime2',
package='qiime2.core.testing',
citation_text='No relevant citation.',
user_support_text='For help, see https://qiime2.org'
)
import_module('qiime2.core.testing.transformer')
# Register semantic types
dummy_plugin.register_semantic_types(IntSequence1, IntSequence2, Mapping,
FourInts, Kennel, Dog, Cat, SingleInt)
# Register formats
dummy_plugin.register_formats(
IntSequenceFormat, IntSequenceFormatV2, MappingFormat, SingleIntFormat,
IntSequenceDirectoryFormat, IntSequenceV2DirectoryFormat,
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import (Plugin, Int, Range, Citations, Str)
from q2_types.feature_data import FeatureData, Sequence
import q2_ipcress
citations = Citations.load('citations.bib', package='q2_ipcress')
plugin = Plugin(
name='ipcress',
version=q2_ipcress.__version__,
website='https://github.com/BenKaehler/q2-ipcress',
package='q2_ipcress',
description=('This QIIME 2 plugin provides support for generating '
'synthetic PCR reads from a set of reference sequences.'),
short_description='Wrapper for ipcress, an in-silico PCR program.')
plugin.methods.register_function(
function=q2_ipcress.ipcress,
inputs={'sequence': FeatureData[Sequence]},
parameters={
'primer_a': Str,
'primer_b': Str,
'min_product_len': Int % Range(0, None),
'max_product_len': Int % Range(0, None),
'mismatch': Int % Range(0, None),
'memory': Int % Range(0, None),
'seed': Int % Range(0, None)
from qiime2.plugin import (Str, Plugin, Choices, Float, Range, Bool)
from q2_types.feature_table import FeatureTable, Frequency
from ._type import Network, PairwiseFeatureData
from ._format import GraphModelingLanguageFormat, GraphModelingLanguageDirectoryFormat, PairwiseFeatureDataFormat, \
PairwiseFeatureDataDirectoryFormat
from ._correlate import calculate_correlations, build_correlation_network_r, build_correlation_network_p
import q2_network
plugin = Plugin(
name='network',
version=q2_network.__version__,
website="https://github.com/shafferm/q2-network",
package='q2_network',
description=(
'This QIIME 2 plugin supports methods for analysis of netwoks '
'generated from correlations or other sources and provides '
'rudimentary network statistics.'),
short_description='Plugin for network analysis.',
)
plugin.register_semantic_types(Network)
plugin.register_semantic_types(PairwiseFeatureData)
plugin.register_formats(GraphModelingLanguageFormat)
plugin.register_formats(GraphModelingLanguageDirectoryFormat)
plugin.register_formats(PairwiseFeatureDataFormat)
plugin.register_formats(PairwiseFeatureDataDirectoryFormat)
plugin.register_semantic_type_to_format(
from qiime2.plugin import Plugin
import qiime2.plugin
from q2_types.feature_table import FeatureTable, Frequency
import q2_metabolomicsgnps
plugin = Plugin(
name='metabolomicsgnps',
version=q2_metabolomicsgnps.__version__,
website='https://gnps.ucsd.edu',
user_support_text='https://gnps.ucsd.edu',
description='Plugin for the creation of a biom feature table for metabolomics data.',
short_description='Plugin for the creation of a biom feature table for metabolomics data.',
package='q2_metabolomicsgnps'
)
plugin.methods.register_function(
function=q2_metabolomicsgnps.gnps_clustering,
inputs={},
parameters={'manifest': qiime2.plugin.Str, 'username': qiime2.plugin.Str, 'password': qiime2.plugin.Str},
input_descriptions={},
outputs=[('feature_table', FeatureTable[Frequency])],
parameter_descriptions={
'manifest': 'Manifest file for describing information about each file. Headers of sample-id and filepath',
'username': '******',
'password': '******'
},
output_descriptions={'feature_table': 'Resulting feature table'},
name='GNPS Metabolomics MS/MS Spectral Counts',
description=("Computes feature BioM for metabolomics using GNPS Molecular Networking"),
citations=[]
)
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import biom
from qiime2.plugin import Plugin
from q2_types.feature_table import FeatureTable, Frequency
import q2_american_gut
plugin = Plugin(
name='american-gut',
version=q2_american_gut.__version__,
website='https://github.com/biocore/q2-american-gut',
package='q2_american_gut',
description=('This QIIME 2 plugin supports processing and utilizing '
'American Gut Project data'),
short_description='Plugin for exploring American Gut data.',
citation_text='https://doi.org/10.1101/277970'
)
def dummy(foo: biom.Table) -> biom.Table:
return foo
plugin.methods.register_function(
function=dummy,
inputs={'foo': FeatureTable[Frequency]},
parameters={},
outputs=[('bar', FeatureTable[Frequency]), ],
input_descriptions={
'foo': "Same same"
SequencesWithQuality,
PairedEndSequencesWithQuality,
)
import q2_cutadapt
import q2_cutadapt._demux
import q2_cutadapt._trim
plugin = Plugin(
name='cutadapt',
version=q2_cutadapt.__version__,
website='https://github.com/qiime2/q2-cutadapt',
package='q2_cutadapt',
description='This QIIME 2 plugin uses cutadapt to work with '
'adapters (e.g. barcodes, primers) in sequence data.',
short_description='Plugin for removing adapter sequences, primers, and '
'other unwanted sequence from sequence data.',
citation_text='Martin, M. (2011). Cutadapt removes adapter sequences from '
'high-throughput sequencing reads. EMBnet.Journal, 17(1), '
'pp. 10-12.\ndoi:http://dx.doi.org/10.14806/ej.17.1.200',
)
plugin.methods.register_function(
function=q2_cutadapt._trim.trim_single,
inputs={
'demultiplexed_sequences': SampleData[SequencesWithQuality],
},
parameters={
'cores': Int % Range(1, None),
'adapter': List[Str],
'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I',
'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5',
'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I',
'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6',
'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G',
'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7',
'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G',
'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8',
'GTR+R9', 'GTR+R10', 'MFP', 'TEST'
]
citations = Citations.load('citations.bib', package='q2_phylogeny')
plugin = Plugin(
name='phylogeny',
version=q2_phylogeny.__version__,
website='https://github.com/qiime2/q2-phylogeny',
package='q2_phylogeny',
description=('This QIIME 2 plugin supports generating and manipulating '
'phylogenetic trees.'),
short_description='Plugin for generating and manipulating phylogenies.')
plugin.methods.register_function(
function=q2_phylogeny.midpoint_root,
inputs={'tree': Phylogeny[Unrooted]},
parameters={},
outputs=[('rooted_tree', Phylogeny[Rooted])],
input_descriptions={'tree': 'The phylogenetic tree to be rooted.'},
parameter_descriptions={},
output_descriptions={'rooted_tree': 'The rooted phylogenetic tree.'},
name='Midpoint root an unrooted phylogenetic tree.',
description=("Midpoint root an unrooted phylogenetic tree."))
import rescript
from rescript._utilities import _rank_handles
from rescript.types._format import (
SILVATaxonomyFormat, SILVATaxonomyDirectoryFormat, SILVATaxidMapFormat,
SILVATaxidMapDirectoryFormat, RNAFASTAFormat, RNASequencesDirectoryFormat)
from rescript.types._type import SILVATaxonomy, SILVATaxidMap, RNASequence
from rescript.types.methods import reverse_transcribe
from rescript.ncbi import get_ncbi_data, _default_ranks, _allowed_ranks
citations = Citations.load('citations.bib', package='rescript')
plugin = Plugin(
name='rescript',
version=rescript.__version__,
website="https://github.com/nbokulich/RESCRIPt",
package='rescript',
description=('Reference sequence annotation and curation pipeline.'),
short_description=(
'Pipeline for reference sequence annotation and curation.'),
)
SILVA_LICENSE_NOTE = (
'NOTE: THIS ACTION ACQUIRES DATA FROM THE SILVA DATABASE. SEE '
'https://www.arb-silva.de/silva-license-information/ FOR MORE INFORMATION '
'and be aware that earlier versions may be released under a different '
'license.')
VOLATILITY_PLOT_XAXIS_INTERPRETATION = (
'The x-axis in these plots represents the taxonomic '
'levels present in the input taxonomies so are labeled numerically '
'instead of by rank, but typically for 7-level taxonomies these will '
from qiime2.plugin import Plugin, Metadata, Str, List, Citations
from q2_types.ordination import PCoAResults
PARAMETERS = {'metadata': Metadata, 'custom_axes': List[Str]}
PARAMETERS_DESC = {
'metadata':
'The sample metadata.',
'custom_axes': ('Numeric sample metadata columns that should be '
'included as axes in the Emperor plot.')
}
plugin = Plugin(
name='emperor',
version=q2_emperor.__version__,
website='http://emperor.microbio.me',
package='q2_emperor',
citations=Citations.load('citations.bib', package='q2_emperor'),
description=('This QIIME 2 plugin wraps Emperor and '
'supports interactive visualization of ordination '
'plots.'),
short_description='Plugin for ordination plotting with Emperor.')
plugin.visualizers.register_function(
function=plot,
inputs={'pcoa': PCoAResults},
parameters={
'metadata': Metadata,
'custom_axes': List[Str]
},
input_descriptions={
'pcoa': 'The principal coordinates matrix to be plotted.'
},
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import q2_ili
from ._plot import plot
from ._semantics import STLDirFmt, Model
from qiime2.plugin import Plugin, Metadata, Citations
plugin = Plugin(
name='ili',
version=q2_ili.__version__,
website='https://ili.embl.de/',
citations=Citations.load('citations.bib', package='q2_ili'),
package='q2_ili',
description=('This QIIME 2 plugin wraps `ili and '
'supports interactive visualization of 3D models'),
short_description='Plugin for spatial mapping with `ili')
# type registration
plugin.register_views(STLDirFmt)
plugin.register_semantic_types(Model)
plugin.register_semantic_type_to_format(Model, artifact_format=STLDirFmt)
plugin.visualizers.register_function(
function=plot,
inputs={'model': Model},
parameters={'metadata': Metadata},
input_descriptions={'model': 'The model where the data will be plotted.'},
import q2_phylogenomics._pipelines
from q2_types.bowtie2 import Bowtie2Index
from q2_types.feature_data import DNASequencesDirectoryFormat
from q2_phylogenomics._format import (GenBankFormat, GenBankDirFmt, BAMFormat,
SAMFormat, BAMFilesDirFmt,
SAMFilesDirFmt, PileUpTSVFormat,
PileUpFilesDirFmt, FASTAFilesDirFmt)
from q2_phylogenomics._types import (AlignmentMap, PileUp, ConsensusSequences,
ReferenceSequence)
citations = Citations.load('citations.bib', package='q2_phylogenomics')
plugin = Plugin(
name='phylogenomics',
version=q2_phylogenomics.__version__,
website='https://github.com/qiime2/q2-phylogenomics',
package='q2_phylogenomics',
description='A QIIME 2 plugin for phylogenomics analyses.',
short_description='A QIIME 2 plugin for phylogenomics analyses.',
)
plugin.register_formats(GenBankFormat, GenBankDirFmt, citations=[])
plugin.register_formats(BAMFormat,
SAMFormat,
BAMFilesDirFmt,
SAMFilesDirFmt,
PileUpTSVFormat,
PileUpFilesDirFmt,
citations=[])
plugin.register_formats(FASTAFilesDirFmt)
plugin.register_semantic_types(AlignmentMap, PileUp, ConsensusSequences,
SequencesWithQuality,
PairedEndSequencesWithQuality,
)
import q2_phylogenomics
import q2_phylogenomics._prinseq
import q2_phylogenomics._filter
from q2_types.bowtie2 import Bowtie2Index
citations = Citations.load('citations.bib', package='q2_phylogenomics')
plugin = Plugin(
name='phylogenomics',
version=q2_phylogenomics.__version__,
website='https://github.com/qiime2/q2-phylogenomics',
package='q2_phylogenomics',
description='A QIIME 2 plugin for phylogenomics analyses.',
short_description='A QIIME 2 plugin for phylogenomics analyses.',
)
prinseq_input = {'demultiplexed_sequences': 'The sequences to be trimmed.'}
prinseq_output = {'trimmed_sequences': 'The resulting trimmed sequences.'}
prinseq_parameters = {
'trim_qual_right': Int % Range(1, None),
'trim_qual_type': Str % Choices(['min', 'mean', 'max', 'sum']),
'trim_qual_window': Int % Range(1, None),
'min_qual_mean': Int % Range(1, None),
'min_len': Int % Range(1, None),
'lc_method': Str % Choices(['dust', 'entropy']),
'lc_threshold': Int % Range(0, 100),
PredictionsDirectoryFormat, ProbabilitiesFormat,
ProbabilitiesDirectoryFormat)
from ._type import (ClassifierPredictions, RegressorPredictions,
SampleEstimator, BooleanSeries, Importance, Classifier,
Regressor, Probabilities)
import q2_sample_classifier
citations = Citations.load('citations.bib', package='q2_sample_classifier')
plugin = Plugin(
name='sample-classifier',
version=q2_sample_classifier.__version__,
website="https://github.com/qiime2/q2-sample-classifier",
package='q2_sample_classifier',
description=(
'This QIIME 2 plugin supports methods for supervised classification '
'and regression of sample metadata, and other supervised machine '
'learning methods.'),
short_description=(
'Plugin for machine learning prediction of sample metadata.'),
citations=[citations['Bokulich306167'], citations['pedregosa2011scikit']])
description = ('Predicts a {0} sample metadata column using a {1}. Splits '
'input data into training and test sets. The training set is '
'used to train and test the estimator using a stratified '
'k-fold cross-validation scheme. This includes optional steps '
'for automated feature extraction and hyperparameter '
'optimization. The test set validates classification accuracy '
'of the optimized estimator. Outputs classification results '
'for test set. For more details on the learning algorithm, '
'see http://scikit-learn.org/stable/supervised_learning.html')
SidleReconFormat,
SidleReconDirFormat,
ReconstructionSummary,
ReconSummaryFormat,
ReconSummaryDirFormat,
)
import q2_sidle
citations = Citations.load('citations.bib', package='q2_sidle')
plugin = Plugin(
name='sidle',
version='2020.08',
website='https://github.com/jwdebelius/q2-sidle',
package='q2_sidle',
description=('This plugin reconstructs a full 16s sequence from short '
'reads over a marker gene region using the Short MUltiple '
'Read Framework (SMURF) algorithm.'),
short_description='Plugin for kmer-based marker gene reconstruction.',
citations=[citations['Debelius2021']],
)
plugin.methods.register_function(
function=q2_sidle.prepare_extracted_region,
name='Prepares an already extracted region to be a kmer database.',
description=('This function takes an amplified region of the database, '
'expands the degenerate sequences and collapses the '
'duplicated sequences under a single id that can be '
'untangled later.'),
inputs={
'sequences': FeatureData[Sequence]
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
from qiime2.plugin import Plugin, Float, Int, Bool, Str, Range, Citations
from q2_types.feature_data import FeatureData, Sequence, AlignedSequence
import q2_alignment
citations = Citations.load('citations.bib', package='q2_alignment')
plugin = Plugin(
name='alignment',
version=q2_alignment.__version__,
website='https://github.com/qiime2/q2-alignment',
package='q2_alignment',
description=('This QIIME 2 plugin provides support for generating '
'and manipulating sequence alignments.'),
short_description='Plugin for generating and manipulating alignments.'
)
plugin.methods.register_function(
function=q2_alignment.mafft,
inputs={'sequences': FeatureData[Sequence]},
parameters={'n_threads': Int % Range(0, None),
'parttree': Bool},
outputs=[('alignment', FeatureData[AlignedSequence])],
input_descriptions={'sequences': 'The sequences to be aligned.'},
parameter_descriptions={
'n_threads': 'The number of threads. (Use 0 to automatically use all '
'available cores)',
# ----------------------------------------------------------------------------
#
#
# ----------------------------------------------------------------------------
from match_samples import match_samples
from qiime2.plugin import (Plugin, Metadata, Str, List, Citations, Range, Int,
Bool, Properties)
from q2_types.ordination import PCoAResults
from q2_types.feature_table import FeatureTable, Frequency, RelativeFrequency
plugin = Plugin(
name='match-samples',
version='1',
package='match_samples',
website='https://github.com/brainiac5mimic/match_samples',
description=('match_samples allows users to filter down a '
'metadata file, label samples case or control, and '
'match case to control samples.'),
short_description=('Filter, label and match samples in a '
'metadata file'))
plugin.visualizers.register_function(
function=match_samples.subsetting,
inputs={},
parameters={
'metadata': Metadata,
'keep': Str,
'extra': Bool,
},
input_descriptions={},
parameter_descriptions={
citations = Citations.load('citations.bib', package='q2_diversity')
sklearn_n_jobs_description = (
'The number of jobs to use for the computation. This works by breaking '
'down the pairwise matrix into n_jobs even slices and computing them in '
'parallel. If -1 all CPUs are used. If 1 is given, no parallel computing '
'code is used at all, which is useful for debugging. For n_jobs below -1, '
'(n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all CPUs but one '
'are used. (Description from sklearn.metrics.pairwise_distances)')
plugin = Plugin(
name='diversity',
version=q2_diversity.__version__,
website='https://github.com/qiime2/q2-diversity',
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)
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.feature_data import FeatureData, Sequence
from q2_ninja_ops import (NinjaOpsDB, NinjaOpsDBDirFmt, Bowtie2IndexFormat,
TerrificCompressedFormat, NinjaReplicateMapFormat,
cluster_closed_reference, build_database)
import q2_ninja_ops
plugin = Plugin(
name='ninja-ops',
version=q2_ninja_ops.__version__,
website='https://github.com/knights-lab/q2-ninja-ops',
package='q2_ninja_ops',
citation_text='Al-Ghalith GA, Montassier E, Ward HN, Knights D. '
'NINJA-OPS: Fast Accurate Marker Gene Alignment Using '
'Concatenated Ribosomes. PLoS Computational Biology. '
'2016 Jan;12(1).',
short_description='Plugin for OTU picking with NINJA-OPS.',
description='This plugin wraps the NINJA-OPS application and provides '
'methods for clustering sequence data into OTUs.'
)
plugin.register_semantic_types(NinjaOpsDB)
plugin.register_formats(NinjaOpsDBDirFmt, Bowtie2IndexFormat,
TerrificCompressedFormat, NinjaReplicateMapFormat)
plugin.register_semantic_type_to_format(NinjaOpsDB,
artifact_format=NinjaOpsDBDirFmt)
