__credits__ = ["Evan Bolyen"]
from pyqi.core.interfaces.optparse.input_handler import command_handler
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload, HTMLPage)
from pyqi.core.interfaces.optparse.input_handler import string_list_handler
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_optparse import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('command'),
Handler=command_handler),
HTMLInputOption(Parameter=cmd_in_lookup('command_module')),
HTMLInputOption(Parameter=cmd_in_lookup('author')),
HTMLInputOption(Parameter=cmd_in_lookup('email')),
HTMLInputOption(Parameter=cmd_in_lookup('license')),
HTMLInputOption(Parameter=cmd_in_lookup('copyright')),
HTMLInputOption(Parameter=cmd_in_lookup('version'),
Name='command-version'),
HTMLInputOption(Parameter=cmd_in_lookup('credits'),
Handler=string_list_handler,
Help='comma-separated list of other authors'),
HTMLInputOption(
Parameter=None,
Name='download-file',
Required=True,
Help=
#-----------------------------------------------------------------------------
__credits__ = ["Evan Bolyen"]
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload, HTMLPage)
from pyqi.core.interfaces.optparse.input_handler import string_list_handler
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_command import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('name')),
HTMLInputOption(Parameter=cmd_in_lookup('author')),
HTMLInputOption(Parameter=cmd_in_lookup('email')),
HTMLInputOption(Parameter=cmd_in_lookup('license')),
HTMLInputOption(Parameter=cmd_in_lookup('copyright')),
HTMLInputOption(Parameter=cmd_in_lookup('version'),
Name='command-version'),
HTMLInputOption(Parameter=cmd_in_lookup('credits'),
Handler=string_list_handler,
Help='comma-separated list of other authors'),
HTMLInputOption(
Parameter=cmd_in_lookup('test_code'),
Type=bool,
Help='Should a stubbed out python test file be generated instead'),
HTMLInputOption(
Parameter=None,
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
def display_table_validity(result_key, data, option_value=None):
if data is None:
return "The input file is a valid BIOM-formatted file."
else:
to_join = ["The input file is not a valid BIOM-formatted file."]
to_join += data
return "<br/>".join(to_join)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('table'),
Type='upload_file',
Handler=load_json_document,
Name='input-fp',
Help='the input file to validate against the BIOM '
'format specification'),
HTMLInputOption(Parameter=cmd_in_lookup('format_version')),
HTMLInputOption(Parameter=cmd_in_lookup('detailed_report'), Type=bool),
]
outputs = [
HTMLPage(Parameter=cmd_out_lookup('report_lines'),
Handler=display_table_validity)
]
__email__ = "*****@*****.**"
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from biom.interfaces.html.input_handler import load_metadata
from biom.commands.table_converter import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('table'),
Type='upload_file',
Help='the input table filepath, either in BIOM or classic '
'format'),
HTMLInputOption(Parameter=cmd_in_lookup('to_tsv'), Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('to_json'), Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('to_hdf5'), Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='upload_file',
Handler=load_metadata),
HTMLInputOption(Parameter=cmd_in_lookup('observation_metadata'),
Type='upload_file',
Handler=load_metadata),
HTMLInputOption(Parameter=cmd_in_lookup('header_key')),
HTMLInputOption(Parameter=cmd_in_lookup('output_metadata_id')),
HTMLInputOption(Parameter=cmd_in_lookup('process_obs_metadata'),
Type='multiple_choice',
Choices=['taxonomy', 'naive', 'sc_separated'],
from biom.commands.table_converter import CommandConstructor
__author__ = "Michael Shaffer"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Michael Shaffer"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Michael Shaffer"
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('biom_table'),
Type='upload_file',
Required=True,
Help='the input table filepath'),
HTMLInputOption(Parameter=cmd_in_lookup('relative_abund'), Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('presence_absence'), Type=bool),
HTMLInputOption(Parameter=cmd_in_lookup('axis'),
Type='multiple_choice',
Choices=['observation', 'sample'],
Help='axis by which to normalize the table'),
HTMLInputOption(Parameter=None,
Name='download-file',
Required=True,
Help='the download file')
]
outputs = [
HTMLDownload(Parameter=cmd_out_lookup('table'),
__email__ = "*****@*****.**"
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload)
from biom.commands.table_summarizer import CommandConstructor
from biom.interfaces.html.input_handler import (
load_biom_table_with_file_contents)
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('table'),
Type="upload_file",
Handler=load_biom_table_with_file_contents,
Name='input-fp'),
HTMLInputOption(Parameter=cmd_in_lookup('qualitative'), Type=bool),
HTMLInputOption(Parameter=None,
Name='download-file',
Required=True,
Help='the download file')
]
outputs = [
HTMLDownload(Parameter=cmd_out_lookup('biom_summary'),
Handler=newline_list_of_strings,
FilenameLookup='download-file',
FileExtension='.biom.summary.txt')
]
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = [
"Evan Bolyen", "Jai Ram Rideout", "Greg Caporaso", "Morgan Langille",
"Daniel McDonald"
]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Evan Bolyen"
__email__ = "*****@*****.**"
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('table'),
Type='upload_file',
Handler=load_biom_table,
Name='input-fp'),
HTMLInputOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='upload_file',
Name='sample-metadata-fp'),
HTMLInputOption(Parameter=cmd_in_lookup('observation_metadata'),
Type='upload_file',
Name='observation-metadata-fp'),
HTMLInputOption(Parameter=cmd_in_lookup('sc_separated'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to '
'split on semicolons. This is useful for hierarchical '
'data such as taxonomy or functional categories'),
HTMLInputOption(Parameter=cmd_in_lookup('sc_pipe_separated'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to split'
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
__credits__ = ["Evan Bolyen"]
from pyqi.core.interfaces.html import (HTMLInputOption, HTMLDownload, HTMLPage)
from pyqi.core.interfaces.html.output_handler import newline_list_of_strings
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from pyqi.commands.make_bash_completion import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
inputs = [
HTMLInputOption(Parameter=cmd_in_lookup('command_config_module')),
HTMLInputOption(Parameter=cmd_in_lookup('driver_name')),
HTMLInputOption(
Parameter=None,
Name='download-file',
Required=True,
Help=
'The name of the bash completion script to download. (e.g. my_file)')
]
outputs = [
HTMLDownload(Parameter=cmd_out_lookup('result'),
FilenameLookup='download-file',
FileExtension='.sh')
]