comparison r_alpha_diversity.xml @ 0:76c750c5f0d1 draft default tip

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" encoding="UTF-8"?>
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 Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="1.0.0">
19 <description>with richness 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_alpha_diversity.py
28 --rdata $data
29 --varExp $varExp
30 --alpha-measures $measures
31 --alpha-out $alphaD
32 --html $html
33 </command>
34 <inputs>
35 <!-- Files -->
36 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
37 <validator type="empty_field" message="This parameter is required." />
38 </param>
39 <!-- Parameters -->
40 <param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
41 <validator type="empty_field" message="This parameter is required." />
42 </param>
43 <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
44 <option value="Observed" selected="True">Observed</option>
45 <option value="Chao1" selected="True">Chao1</option>
46 <option value="Shannon" selected="True">Shannon</option>
47 <option value="InvSimpson" selected="True">InvSimpson</option>
48 <option value="Simpson">Simpson</option>
49 <option value="ACE">ACE</option>
50 <option value="Fisher">Fisher</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
55 <data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="data" value="references/11-phylo_import.Rdata" />
60 <param name="varExp" value="EnvType" />
61 <param name="measures" value="Observed,Chao1,Shannon" />
62 <output name="alphaD" file="references/13-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
63 </test>
64 </tests>
65 <help>
66
67 .. image:: static/images/FROGS_logo.png
68 :height: 144
69 :width: 110
70
71 .. class:: infomark page-header h2
72
73 What it does
74
75 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity.
76
77 .. class:: infomark page-header h2
78
79 Inputs/Outputs
80
81 .. class:: h3
82
83 Input
84
85 **Data file** (format RData):
86 One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata.
87 This file is the result of "FROGS Phyloseq Import Data tool".
88
89 .. class:: h3
90
91 Output
92
93 **Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): the review of richness plots and rarefaction curves.
94
95 .. image:: static/images/phyloseq_plot_richness.png
96 :height: 400
97 :width: 525
98
99 .. image:: static/images/phyloseq_plot_richness_box.png
100 :height: 400
101 :width: 499
102
103 .. image:: static/images/phyloseq_rarefaction_curves.png
104 :height: 400
105 :width: 498
106
107 **Alpha diversity table** (alpha_diversity.tsv):
108 The data file containing table of alpha diversity indices.
109
110 .. image:: static/images/phyloseq_alpha_diversity_table.png
111
112 .. class:: infomark page-header h2
113
114 **Contact**
115
116 Contacts: frogs@inra.fr
117
118 Repository: https://github.com/geraldinepascal/FROGS
119
120 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
121
122 Depending on the help provided you can cite us in acknowledgements, references or both.
123
124 </help>
125 <citations>
126 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
127 </citations>
128 </tool>