forked from geraldinepascal/FROGS-wrappers
-
Notifications
You must be signed in to change notification settings - Fork 0
/
r_alpha_diversity.xml
executable file
·127 lines (104 loc) · 4.82 KB
/
r_alpha_diversity.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
123
124
125
126
127
<?xml version="1.0" encoding="UTF-8"?>
<!--
# Copyright (C) 2017 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 name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.1">
<description>with richness plot</description>
<requirements>
<requirement type="package" version="3.1.0">frogs</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
</stdio>
<command>r_alpha_diversity.py
--rdata $data
--varExp $varExp
--alpha-measures $measures
--alpha-out $alphaD
--html $html
</command>
<inputs>
<!-- Files -->
<param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
<validator type="empty_field" message="This parameter is required." />
</param>
<!-- Parameters -->
<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
<validator type="empty_field" message="This parameter is required." />
</param>
<param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
<option value="Observed" selected="True">Observed</option>
<option value="Chao1" selected="True">Chao1</option>
<option value="Shannon" selected="True">Shannon</option>
<option value="InvSimpson" selected="True">InvSimpson</option>
<option value="Simpson">Simpson</option>
<option value="ACE">ACE</option>
<option value="Fisher">Fisher</option>
</param>
</inputs>
<outputs>
<data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
<data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
</outputs>
<tests>
<test>
<param name="data" value="references/14-phylo_import.Rdata" />
<param name="varExp" value="EnvType" />
<param name="measures" value="Observed,Chao1,Shannon" />
<output name="alphaD" file="references/16-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
</test>
</tests>
<help>
.. image:: static/images/frogs_images/FROGS_logo.png
:height: 144
:width: 110
.. class:: infomark page-header h2
What it does
Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity.
.. class:: infomark page-header h2
Inputs/Outputs
.. class:: h3
Input
**Data file** (format RData):
One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata.
This file is the result of "FROGS Phyloseq Import Data tool".
.. class:: h3
Output
**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves.
.. image:: static/images/frogs_images/phyloseq_plot_richness.png
:height: 400
:width: 525
.. image:: static/images/frogs_images/phyloseq_plot_richness_box.png
:height: 400
:width: 499
.. image:: static/images/frogs_images/phyloseq_rarefaction_curves.png
:height: 400
:width: 498
**Alpha diversity table** (alpha_diversity.tsv):
The data file containing table of alpha diversity indices.
.. image:: static/images/frogs_images/phyloseq_alpha_diversity_table.png
.. class:: infomark page-header h2
**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>