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)