forked from geraldinepascal/FROGS-wrappers
-
Notifications
You must be signed in to change notification settings - Fork 0
/
normalisation.xml
122 lines (90 loc) · 4.01 KB
/
normalisation.xml
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
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
<?xml version="1.0"?>
<!--
# Copyright (C) 2015 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="3.1">
<description>Normalize OTUs abundance.</description>
<requirements>
<requirement type="package" version="3.1.0">frogs</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
</stdio>
<command>
normalisation.py
--input-biom $input_biom
--input-fasta $input_fasta
--num-reads $num_reads
--output-biom $output_biom
--output-fasta $output_fasta
--summary-file $summary_file
</command>
<inputs>
<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
<param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
</inputs>
<outputs>
<data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
<data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
</outputs>
<tests>
<test>
<param name="input_fasta" value="references/04-filters.fasta"/>
<param name="input_biom" value="references/06-affiliation.biom"/>
<param name="num_reads" value="100"/>
<output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" />
</test>
</tests>
<help>
.. image:: static/images/frogs_images/FROGS_logo.png
:height: 144
:width: 110
.. class:: infomark page-header h2
What it does
This tool keeps, in each sample, the same number of elements by random sampling.
.. class:: infomark page-header h2
Inputs/outputs
.. class:: h3
Inputs
**Sequence file**:
The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
**Abundance file**:
The abundance of each OTU in each sample (format `BIOM <http://biom-format.org/>`_).
.. class:: h3
Outputs
**Sequence file** (normalised_seed.fasta):
The normalised sequences file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
**Abundance file** (normalised_abundance.biom):
The normalised abundance file (format `BIOM <http://biom-format.org/>`_).
**Summary file** (report.html):
Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).
.. class:: infomark page-header h2
Advices
The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
----
**Contact**
Contacts: [email protected]
Repository: https://github.com/geraldinepascal/FROGS
website: http://frogs.toulouse.inra.fr/
Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btx791</citation>
</citations>
</tool>