__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') ]