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planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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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 Structure Visualisation" id="FROGSSTAT_Phyloseq_Structure_Visualisation" version="1.0.0">
19 <description>with heatmap plot and ordination plot</description>
20 <requirements>
21 <requirement type="package" version="2.0.1">frogs</requirement>
22 </requirements>
23 <stdio>
24 <exit_code range="1:" />
25 <exit_code range=":-1" />
26 </stdio>
27 <command>r_structure.py
28 --html $html
29 --rdata $data
30 --varExp $varExp
31 --ordination-method $method
32 --distance-matrix $distance
33 </command>
34 <inputs>
35 <!-- Files -->
36 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data Tool." optional="false">
37 <validator type="empty_field" message="This parameter is required." />
38 </param>
39 <param name="distance" format="tabular" type="data" label="The beta diversity distance matrix file" help="These file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
40 <validator type="empty_field" message="This parameter is required." />
41 </param>
42 <!-- Parameters -->
43 <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
44 <validator type="empty_field" message="This parameter is required." />
45 </param>
46 <param name="method" type="select" label="Ordination method">
47 <option value="MDS" >MDS/PCoA</option>
48 <option value="NMDS" >NMDS</option>
49 <option value="DPCoA" >DPCoA</option>
50 </param>
51 </inputs>
52 <outputs>
53 <data format="html" name="html" label="${tool.name}: structure.html" from_work_dir="structure.html"/>
54 </outputs>
55 <tests>
56 <test>
57 <param name="data" value="references/11-phylo_import.Rdata" />
58 <param name="varExp" value="EnvType" />
59 <param name="method" value="MDS" />
60 <param name="distance" value="references/Unifrac.tsv" />
61 <!--output name="html" file="references/15-phylo_structure.html" compare="sim_size" delta="10" /-->
62 <output name="html">
63 <assert_contents>
64 <has_text_matching expression="html\sxmlns=.*" />
65 <has_text_matching expression="application/json.*DesLardons" />
66 </assert_contents>
67 </output>
68
69 </test>
70 </tests>
71 <help>
72
73 .. image:: static/images/FROGS_logo.png
74 :height: 144
75 :width: 110
76
77 .. class:: infomark page-header h2
78
79 What it does
80
81 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods &lt;https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods&gt;`_ to visualise data structure.
82
83 .. class:: infomark page-header h2
84
85 Inputs/Outputs
86
87 .. class:: h3
88
89 Input
90
91 **data file** (format rdata):
92 The informations of data in one phyloseq object.
93 This file is the result of "FROGS Phyloseq Import Data tool".
94
95 **distance file** (format tabular):
96 The data file containing beta diversity distance matrix.
97 This file is the result of "FROGS Phyloseq Beta Diversity tool".
98
99 .. class:: h3
100
101 Output
102
103 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
104
105 The review of data structure with an ordination plot and with an heatmap plot:
106
107 .. image:: static/images/phyloseq_plot_sample_ellipse.png
108 :height: 343
109 :width: 450
110
111 .. image:: static/images/phyloseq_plot_heatmap_red.png
112 :height: 343
113 :width: 450
114
115 .. class:: infomark page-header h2
116
117 **Contact**
118
119 Contacts: frogs@inra.fr
120
121 Repository: https://github.com/geraldinepascal/FROGS
122
123 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf
124
125 Depending on the help provided you can cite us in acknowledgements, references or both.
126
127 </help>
128 <citations>
129 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
130 </citations>
131 </tool>