1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
#!/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.
# -----------------------------------------------------------------------------
__author__ = "Evan Bolyen"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = [
"Evan Bolyen",
"Greg Caporaso",
"Jai Ram Rideout",
"Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Evan Bolyen"
__email__ = "ebolyen@gmail.com"
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')
]
|
