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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 id="FROGSSTAT_Phyloseq_Composition_Visualisation" name="FROGSSTAT Phyloseq Composition Visualisation" version="3.1">
19 <description>with bar plot and composition plot</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_composition.py
28 --rdata $data
29 --varExp $varExp
30 --taxaRank1 $taxaRank1
31 --taxaSet1 $taxaSet1
32 --taxaRank2 $taxaRank2
33 --numberOfTaxa $numberOfTaxa
34 --html $html
35 </command>
36 <inputs>
37 <!-- Files -->
38 <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
39 <validator type="empty_field" message="This parameter is required." />
40 </param>
41 <!-- Parameters -->
42 <param name="varExp" type="text" label="Grouping variable" help="Experimental variable used to group samples (Treatment, Host type, etc)." optional="false" value="" size="20">
43 <validator type="empty_field" message="This parameter is required." />
44 </param>
45 <param name="taxaRank1" type="text" label="Taxonomic level to filter your data" help="ex: Kingdom, Phylum, Class, Order, Family, Genus, Species" value="Kingdom" size="20">
46 <validator type="empty_field" message="This parameter is required." />
47 </param>
48 <param name="taxaSet1" type="text" label="Taxa (at the above taxonomic level) to keep in the dataset" help="ex: Bacteria (when filtering at the Kingdom level), Firmicutes (when filtering at the Phylum level). Multiple taxa (separated by a space) can be specified, i.e. Firmicutes Proteobacteria" value="Bacteria" size="20">
49 <validator type="empty_field" message="This parameter is required." />
50 </param>
51 <param name="taxaRank2" type="text" label="Taxonomic level used for aggregation" help="ex: Family (when filtering at the Phylum level). The aggregation level must be below the filtering level." value="Phylum" size="20">
52 <validator type="empty_field" message="This parameter is required." />
53 </param>
54 <param name="numberOfTaxa" type="text" label="Number of most abundant taxa to keep" help="ex: 9, i.e. Tool keeps the 9 most abundant taxa and the remaining taxa are aggregated in a group 'Other'" value="9" size="20">
55 <validator type="empty_field" message="This parameter is required." />
56 </param>
57 </inputs>
58 <outputs>
59 <data format="html" name="html" label="${tool.name}: composition.html" from_work_dir="composition.html"/>
60 </outputs>
61 <tests>
62 <test>
63 <param name="data" value="references/14-phylo_import.Rdata" />
64 <param name="varExp" value="EnvType" />
65 <param name="taxaRank1" value="Kingdom" />
66 <param name="taxaSet1" value="Bacteria" />
67 <param name="taxaRank2" value="Phylum" />
68 <param name="numberOfTaxa" value="9" />
69 <!--output name="html" file="references/15-phylo_composition.html" compare="sim_size" delta="0" /-->
70 <output name="html">
71 <assert_contents>
72 <has_text_matching expression="html\sxmlns=.*" />
73 <has_text_matching expression="application/json.*Sample: BHT0.LOT01" />
74 </assert_contents>
75 </output>
76 </test>
77 </tests>
78 <help>
79 .. image:: static/images/frogs_images/FROGS_logo.png
80 :height: 144
81 :width: 110
82
83 .. class:: infomark page-header h2
84
85 What it does
86
87 Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots.
88
89
90 .. class:: infomark page-header h2
91
92 Inputs/Outputs
93
94 .. class:: h3
95
96 Input
97
98 **data file** (format rdata):
99 One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata.
100 this file is the result of FROGS Phyloseq Import Data tool.
101
102 .. class:: h3
103
104 Output
105
106 **html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): data composition plots.
107
108 Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" :
109
110 .. image:: static/images/frogs_images/phyloseq_bar_plot.png
111 :height: 646
112 :width: 800
113
114 Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs.
115
116 - Selection of OTUs:
117
118 - Taxonomic level name to subset: Kingdom
119 - Taxon name: Bacteria
120
121 - Aggregation of OTUs :
122
123 - Taxonomic level used to agglomerate: Phylum
124
125 - Number of the most abundant taxa to keep: 5
126
127 .. image:: static/images/frogs_images/phyloseq_composition_plot.png
128 :height: 644
129 :width: 800
130
131 .. class:: infomark page-header h2
132
133 **Contact**
134
135 Contacts: frogs@inra.fr
136
137 Repository: https://github.com/geraldinepascal/FROGS
138 website: http://frogs.toulouse.inra.fr/
139
140 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
141
142 </help>
143 <citations>
144 <citation type="doi">10.1093/bioinformatics/btx791</citation>
145 </citations>
146
147 </tool>