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)
plugin.register_views(ZodiacDirFmt)
plugin.register_semantic_types(ZodiacFolder)
plugin.register_semantic_type_to_format(ZodiacFolder,
artifact_format=ZodiacDirFmt)
plugin.register_views(CSIDirFmt)
# Register formats
dummy_plugin.register_formats(IntSequenceFormatV2, MappingFormat,
IntSequenceV2DirectoryFormat,
IntSequenceMultiFileDirectoryFormat,
MappingDirectoryFormat, EchoDirectoryFormat,
EchoFormat)
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(
IntSequence3, artifact_format=IntSequenceMultiFileDirectoryFormat)
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)
# ----------------------------------------------------------------------------
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.'},
parameter_descriptions={'metadata': 'Metadata used to color the model'},
name='Visualize and interact with 3D models',
description='Visualize and interact with 3D models colored using metadata')
# 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)
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(
from ._shogun import minipipe, nobunaga
import q2_shogun
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)
from qiime2.plugin import Plugin, Str, Range, Choices, Float, Int
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.tree import Phylogeny, Rooted
plugin = Plugin(
name='chemistree',
version='0.0.0',
website='https://github.com/biocore/q2-chemistree',
package='q2_chemistree',
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)
PARAMS = {
'database': Str % Choices(['all', 'pubchem']),
'sirius_path': Str,
'profile': Str % Choices(['qtof', 'orbitrap', 'fticr']),
'fingerid_db': Str % Choices(['all', 'pubchem', 'bio', 'kegg', 'hmdb']),
'ppm_max': Int % Range(0, 30, inclusive_end=True),
'n_jobs': Int % Range(1, None),
'num_candidates': Int % Range(5, 100, inclusive_end=True),
'tree_timeout': Int % Range(600, 3000, inclusive_end=True),
'maxmz': Int % Range(100, 850, inclusive_end=True),
'zodiac_threshold': Float % Range(0, 1, inclusive_end=True),
from qiime2.plugin import Plugin, Str, Range, Choices, Float, Int, Bool
from q2_types.feature_table import FeatureTable, Frequency
from q2_types.tree import Phylogeny, Rooted
import importlib
plugin = Plugin(
name='chemistree',
version='0.0.0',
website='https://github.com/biocore/q2-chemistree',
package='q2_chemistree',
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)
plugin.register_views(ZodiacDirFmt)
plugin.register_semantic_types(ZodiacFolder)
plugin.register_semantic_type_to_format(ZodiacFolder,
artifact_format=ZodiacDirFmt)
plugin.register_views(CSIDirFmt)
