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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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1 <?xml version="1.0"?>
2 <!--
3 # Copyright (C) 2017 INRA
4 #
5 # This program is free software: you can redistribute it and/or modify
6 # it under the terms of the GNU General Public License as published by
7 # the Free Software Foundation, either version 3 of the License, or
8 # (at your option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14 #
15 # You should have received a copy of the GNU General Public License
16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
17 -->
18 <tool name="FROGSSTAT Phyloseq Multivariate Analysis Of Variance" id="FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance" version="3.1">
19 <description>perform Multivariate Analysis of Variance (MANOVA)</description>
20 <requirements>
21 <requirement type="package" version="3.1.0">frogs</requirement>
22 </requirements>
23 <stdio>
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <command>r_manova.py
28 --rdata $data
29 --varExp "$varExp"
30 --distance-matrix $method
31 --html $html
32 </command>
33 <inputs>
34 <!-- Files -->
35 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
36 <validator type="empty_field" message="This parameter is required." />
37 </param>
38 <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
39 <validator type="empty_field" message="This parameter is required." />
40 </param>
41 <!-- Parameters -->
42 <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
43 <validator type="empty_field" message="This parameter is required." />
44 </param>
45 </inputs>
46 <outputs>
47 <data format="html" name="html" label="${tool.name}: manova.html" from_work_dir="manova.html"/>
48 </outputs>
49 <tests>
50 <test>
51 <param name="data" value="references/14-phylo_import.Rdata"/>
52 <param name="varExp" value="EnvType"/>
53 <param name="method" value="references/Unifrac.tsv"/>
54 <!--output name="html" file="references/20-phylo_structure.html" compare="sim_size" delta="0" /-->
55 <output name="html">
56 <assert_contents>
57 <has_text_matching expression="html\sxmlns=.*" />
58 <has_text_matching expression="Phyloseq\s+\d+\.\d+\.\d+" />
59 </assert_contents>
60 </output>
61 </test>
62 </tests>
63 <help>
64
65 .. image:: static/images/frogs_images/FROGS_logo.png
66 :height: 144
67 :width: 110
68
69 .. class:: infomark page-header h2
70
71 What it does
72
73 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and `vegan &lt;https://cran.r-project.org/web/packages/vegan/index.html&gt;`_ functions to perform Multivariate Analysis of Variance (MANOVA)
74
75 .. class:: infomark page-header h2
76
77 Inputs/Outputs
78
79 .. class:: h3
80
81 Input
82
83 **data file** (format RData):
84 The informations of data in one phyloseq object.
85 This is the result of FROGS Phyloseq Import Data tool.
86
87 **distance file** (format tabular):
88 The data file containing beta diversity distance matrix.
89 This file is the result of FROGS Phyloseq Beta Diversity tool.
90
91 .. class:: h3
92
93 Output
94
95 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The review of Manova test.
96
97 .. image:: static/images/frogs_images/phyloseq_manova.png
98
99 .. class:: infomark page-header h2
100
101 **Contact**
102
103 Contacts: frogs@inra.fr
104
105 Repository: https://github.com/geraldinepascal/FROGS
106 website: http://frogs.toulouse.inra.fr/
107
108 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
109
110 </help>
111 <citations>
112 <citation type="doi">10.1093/bioinformatics/btx791</citation>
113 </citations>
114
115 </tool>