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#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2013, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
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 pyqi.core.interfaces.optparse.input_handler import string_list_handler
from biom.interfaces.html.input_handler import load_biom_table
from biom.commands.metadata_adder import CommandConstructor
__author__ = "Evan Bolyen"
__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__ = "ebolyen@gmail.com"
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'
' on semicolons and pipes ("|"). This is useful for '
'hierarchical data such as functional categories with '
'one-to-many mappings (e.g. x;y;z|x;y;w)'),
HTMLInputOption(Parameter=cmd_in_lookup('int_fields'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to cast '
'to integers. This is useful for integer data such as '
'"DaysSinceStart"'),
HTMLInputOption(Parameter=cmd_in_lookup('float_fields'),
Handler=string_list_handler,
Help='comma-separated list of the metadata fields to cast '
'to floating point numbers. This is useful for real number'
' data such as "pH"'),
HTMLInputOption(Parameter=cmd_in_lookup('sample_header'),
Handler=string_list_handler,
Help='comma-separated list of the sample metadata field '
'names. This is useful if a header line is not provided '
'with the metadata, if you want to rename the fields, or '
'if you want to include only the first n fields where n is'
' the number of entries provided here'),
HTMLInputOption(Parameter=cmd_in_lookup('observation_header'),
Handler=string_list_handler,
Help='comma-separated list of the observation metadata '
'field names. This is useful if a header line is not '
'provided with the metadata, if you want to rename the '
'fields, or if you want to include only the first n fields'
' where n is the number of entries provided here'),
HTMLInputOption(Parameter=None,
Name='download-file',
Required=True,
Help='the download file')
]
outputs = [
HTMLDownload(Parameter=cmd_out_lookup('table'),
Handler=newline_list_of_strings,
FilenameLookup='download-file',
FileExtension='.biom')
]
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