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)
plugin.methods.register_function(
function=cluster_closed_reference,
inputs={
'sequences': SampleData[Sequences],
'reference_database': NinjaOpsDB
},
parameters={
# TODO expose relevant NINJA-OPS parameters here
},
outputs=[
('clustered_table', FeatureTable[Frequency]),
('unmatched_sequences', SampleData[Sequences])
],
input_descriptions={
# Register formats
dummy_plugin.register_formats(
IntSequenceFormatV2, MappingFormat, IntSequenceV2DirectoryFormat,
MappingDirectoryFormat)
dummy_plugin.register_formats(
FourIntsDirectoryFormat, UnimportableDirectoryFormat, UnimportableFormat,
citations=[citations['baerheim1994effect']])
dummy_plugin.register_views(
int, IntSequenceFormat, IntSequenceDirectoryFormat,
SingleIntFormat, RedundantSingleIntDirectoryFormat,
citations=[citations['mayer2012walking']])
dummy_plugin.register_semantic_type_to_format(
IntSequence1,
artifact_format=IntSequenceDirectoryFormat
)
dummy_plugin.register_semantic_type_to_format(
IntSequence2,
artifact_format=IntSequenceV2DirectoryFormat
)
dummy_plugin.register_semantic_type_to_format(
Mapping,
artifact_format=MappingDirectoryFormat
)
dummy_plugin.register_semantic_type_to_format(
FourInts,
artifact_format=FourIntsDirectoryFormat
)
dummy_plugin.register_semantic_type_to_format(
SingleInt,
'formula': Str,
'learning_rate': Float,
'beta1': Float,
'beta2': Float
},
outputs=[('differentials', FeatureData[Differential]),
('posterior', StrayPosterior)],
input_descriptions={
'table': 'The feature table of abundances.'
},
parameter_descriptions={
'metadata': 'Sample metadata',
'formula': 'The experimental condition of interest.',
'learning_rate': 'The learning rate of the gradient descent.',
'beta1': 'First momentum operator in ADAM gradient descent',
'beta2': 'Second momentum operator in ADAM gradient descent'
},
output_descriptions={
'differentials': 'The estimated per-feature differentials.',
'posterior': 'The posterior distribution over all of the differentials.'
}
)
# TODO: Need to add a visualizer to summarize the stray results
plugin.register_formats(StrayPosteriorFormat, StrayPosteriorDirFmt)
plugin.register_semantic_types(StrayPosterior)
plugin.register_semantic_type_to_format(
StrayPosterior, StrayPosteriorDirFmt)
importlib.import_module('q2_stray._transformer')
SBMLDirectory,
JSONFormat,
JSONDirectory,
CommunityModelFormat,
CommunityModelManifest,
CommunityModelDirectory,
GrowthRates,
Fluxes,
MicomResultsDirectory,
MicomMediumFile,
MicomMediumDirectory,
TradeoffResultsDirectory,
)
plugin.register_semantic_types(MetabolicModels, CommunityModels, MicomResults,
MicomMedium)
plugin.register_semantic_type_to_format(MetabolicModels[SBML], SBMLDirectory)
plugin.register_semantic_type_to_format(MetabolicModels[JSON], JSONDirectory)
plugin.register_semantic_type_to_format(CommunityModels[Pickle],
CommunityModelDirectory)
plugin.register_semantic_type_to_format(MicomResults, MicomResultsDirectory)
plugin.register_semantic_type_to_format(TradeoffResults,
TradeoffResultsDirectory)
plugin.register_semantic_type_to_format(MicomMedium[Global],
MicomMediumDirectory)
plugin.register_semantic_type_to_format(MicomMedium[PerSample],
MicomMediumDirectory)
plugin.methods.register_function(
function=q2_micom.db,
inputs={},
parameters={
citations = Citations.load('citations.bib', package='q2_shogun')
plugin = Plugin(
name='shogun',
version=q2_shogun.__version__,
website='https://github.com/qiime2/q2-shogun',
package='q2_shogun',
description=('A QIIME 2 plugin wrapper for the SHOGUN shallow shotgun '
'sequencing taxonomy profiler.'),
short_description='Shallow shotgun sequencing taxonomy profiler.',
citations=[citations['Hillmann320986']])
plugin.register_views(Bowtie2IndexDirFmt,
citations=[citations['langmead2012fast']])
plugin.register_semantic_types(Bowtie2Index)
plugin.register_semantic_type_to_format(Bowtie2Index, Bowtie2IndexDirFmt)
plugin.methods.register_function(
function=nobunaga,
inputs={
'query': FeatureData[Sequence],
'reference_reads': FeatureData[Sequence],
'reference_taxonomy': FeatureData[Taxonomy],
'database': Bowtie2Index
},
parameters={
'taxacut': Float % Range(0.0, 1.0, inclusive_end=True),
'threads': Int % Range(1, None),
'percent_id': Float % Range(0.0, 1.0, inclusive_end=True)
},
outputs=[('taxa_table', FeatureTable[Frequency])],
'Heatmap of important features.',
'filtered_table':
'Filtered feature table containing data displayed '
'in heatmap.'
},
name='Generate heatmap of important features.',
description='Generate a heatmap of important features. Features are '
'filtered based on importance scores; samples are optionally '
'grouped by metadata; and a heatmap is generated that '
'displays (normalized) feature abundances per sample.')
# Registrations
plugin.register_semantic_types(SampleEstimator, BooleanSeries, Importance,
ClassifierPredictions, RegressorPredictions,
Classifier, Regressor)
plugin.register_semantic_type_to_format(SampleEstimator[Classifier],
artifact_format=SampleEstimatorDirFmt)
plugin.register_semantic_type_to_format(SampleEstimator[Regressor],
artifact_format=SampleEstimatorDirFmt)
plugin.register_semantic_type_to_format(
SampleData[BooleanSeries], artifact_format=BooleanSeriesDirectoryFormat)
plugin.register_semantic_type_to_format(
SampleData[RegressorPredictions],
artifact_format=PredictionsDirectoryFormat)
plugin.register_semantic_type_to_format(
SampleData[ClassifierPredictions],
artifact_format=PredictionsDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[Importance], artifact_format=ImportanceDirectoryFormat)
plugin.register_formats(SampleEstimatorDirFmt, BooleanSeriesFormat,
BooleanSeriesDirectoryFormat, ImportanceFormat,
ImportanceDirectoryFormat, PredictionsFormat,
IntSequenceV2DirectoryFormat,
MappingDirectoryFormat)
dummy_plugin.register_formats(FourIntsDirectoryFormat,
UnimportableDirectoryFormat,
UnimportableFormat,
citations=[citations['baerheim1994effect']])
dummy_plugin.register_views(int,
IntSequenceFormat,
IntSequenceDirectoryFormat,
SingleIntFormat,
RedundantSingleIntDirectoryFormat,
citations=[citations['mayer2012walking']])
dummy_plugin.register_semantic_type_to_format(
IntSequence1, artifact_format=IntSequenceDirectoryFormat)
dummy_plugin.register_semantic_type_to_format(
IntSequence2, artifact_format=IntSequenceV2DirectoryFormat)
dummy_plugin.register_semantic_type_to_format(
Mapping, artifact_format=MappingDirectoryFormat)
dummy_plugin.register_semantic_type_to_format(
FourInts, artifact_format=FourIntsDirectoryFormat)
dummy_plugin.register_semantic_type_to_format(
SingleInt, artifact_format=RedundantSingleIntDirectoryFormat)
dummy_plugin.register_semantic_type_to_format(
Kennel[Dog | Cat], artifact_format=MappingDirectoryFormat)
# TODO add an optional parameter to this method when they are supported
dummy_plugin.methods.register_function(
function=concatenate_ints,
inputs={
def create_plugin(**filters):
plugin = Plugin(
name='mystery-stew',
project_name='q2-mystery-stew',
version=q2_mystery_stew.__version__,
website='https://github.com/qiime2/q2-mystery-stew',
package='q2_mystery_stew',
description=('This QIIME 2 plugin templates out arbitrary '
'QIIME 2 actions to test interfaces. '),
short_description='Plugin for generating arbitrary QIIME 2 '
'actions.')
plugin.register_semantic_types(SingleInt1, SingleInt2, IntWrapper,
WrappedInt1, WrappedInt2, EchoOutput)
plugin.register_formats(SingleIntFormat, SingleIntDirectoryFormat,
EchoOutputFmt, EchoOutputDirFmt)
plugin.register_semantic_type_to_format(SingleInt1,
SingleIntDirectoryFormat)
plugin.register_semantic_type_to_format(SingleInt2,
SingleIntDirectoryFormat)
plugin.register_semantic_type_to_format(
IntWrapper[WrappedInt1 | WrappedInt2], SingleIntDirectoryFormat)
plugin.register_semantic_type_to_format(EchoOutput, EchoOutputDirFmt)
# This transformer is being registered in this file right now because it is
# needed by the registration functions so it needs to be registered before
# it is called
@plugin.register_transformer
def _0(data: int) -> SingleIntFormat:
ff = SingleIntFormat()
with ff.open() as fh:
fh.write('%d\n' % data)
return ff
selected_types = []
basics = {
'ints': int_params,
'floats': float_params,
'strings': string_params,
'bools': bool_params,
'metadata': simple_metadata,
'primitive_unions': primitive_unions,
'artifacts': artifact_params
}
for key, generator in basics.items():
if not filters or filters.get(key, False):
selected_types.append(generator())
if not filters or filters.get('collections', False):
if key != 'metadata':
selected_types.append(list_params(generator()))
selected_types.append(set_params(generator()))
if not selected_types:
raise ValueError("Must select at least one parameter type to use")
register_single_type_tests(plugin, selected_types)
return plugin
plugin = Plugin(name='genome-sampler',
website='https://caporasolab.us/genome-sampler',
package='genome_sampler',
version=genome_sampler.__version__,
description='Tools for sampling from collections of genomes.',
short_description='Genome sampler.',
citations=[citations['genomesampler']])
plugin.register_formats(IDSelectionDirFmt)
plugin.register_formats(GISAIDDNAFASTAFormat)
plugin.register_formats(VCFMaskFormat)
plugin.register_formats(VCFMaskDirFmt)
plugin.register_semantic_types(Selection)
plugin.register_semantic_types(AlignmentMask)
plugin.register_semantic_type_to_format(FeatureData[Selection],
artifact_format=IDSelectionDirFmt)
plugin.register_semantic_type_to_format(AlignmentMask,
artifact_format=VCFMaskDirFmt)
@plugin.register_transformer
def _1(obj: IDSelection) -> IDSelectionDirFmt:
result = IDSelectionDirFmt()
inclusion = obj.inclusion
assert not inclusion.index.has_duplicates
include = inclusion.index[inclusion]
exclude = inclusion.index[~inclusion]
with open(result.included.path_maker(), 'w') as fh:
fh.write('\n'.join(include))
from qiime2.plugin import Plugin, SemanticType
from q2_types.feature_table import FeatureTable, RelativeFrequency, BIOMV210DirFmt
from q2_sqrt.action import square_root
plugin = Plugin("sqrt",
version="0.0.1.dev",
website="google.com",
package="q2_sqrt")
SquareRoot = SemanticType('SquareRoot',
variant_of=FeatureTable.field['content'])
plugin.register_semantic_types(SquareRoot)
plugin.register_semantic_type_to_format(FeatureTable[SquareRoot],
BIOMV210DirFmt)
plugin.methods.register_function(
square_root,
name="Square Root Transform",
description="Convert a table from relative frequency to square root",
inputs={"table": FeatureTable[RelativeFrequency]},
parameters={},
outputs=[("sqrt_table", FeatureTable[SquareRoot])],
input_descriptions={"table": "A relative frequency table"},
output_descriptions={'sqrt_table': 'The transformed table'})
citations = Citations.load('citations.bib', package='q2_qemistree')
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.',
citations=citations,
)
# 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)
plugin.register_views(ZodiacDirFmt)
plugin.register_semantic_types(ZodiacFolder)
plugin.register_semantic_type_to_format(ZodiacFolder,
artifact_format=ZodiacDirFmt)
plugin.register_views(CSIDirFmt)
plugin.register_semantic_types(CSIFolder)
plugin.register_semantic_type_to_format(CSIFolder,
artifact_format=CSIDirFmt)
