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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="FROGS_Tree" name="FROGS Tree" version="3.1">
19 <description>Reconstruction of phylogenetic tree </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>tree.py
28 --input-otu $input_otu
29 --biomfile $biomfile
30 --nb-cpus \${GALAXY_SLOTS:-1}
31 --out-tree $out_tree
32 --html $html
33 </command>
34 <inputs>
35 <!-- Files -->
36 <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
37 <validator type="empty_field" message="This parameter is required." />
38 </param>
39 <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
40 <validator type="empty_field" message="This parameter is required." />
41 </param>
42 </inputs>
43 <outputs>
44 <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
45 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="input_otu" value="references/04-filters.fasta"/>
50 <param name="biomfile" value="references/06-affiliation.biom"/>
51 <!--output name="out_tree" value="references/13-tree-mafft.nwk"/-->
52 <!--output name="html" value="references/13-tree-mafft.html"/-->
53 <output name="html">
54 <assert_contents>
55 <has_text_matching expression="FROGS\sTree" />
56 <has_text_matching expression="abundance_removed.*:\s0" />
57 <has_text_matching expression="abundance_kept.*:\s45574" />
58 <has_text_matching expression="otu_removed.*:\s0" />
59 <has_text_matching expression="otu_kept.*:\s86" />
60 </assert_contents>
61 </output>
62 </test>
63 </tests>
64 <help>
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 Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
74 And creation of a rooted phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_ and `Phangorn R package &lt;https://cran.r-project.org/web/packages/phangorn/index.html&gt;`_.
75
76 .. class:: infomark page-header h2
77
78 Inputs/Outputs
79
80 .. class:: h3
81
82 Input
83
84 **OTUs fasta file**:
85
86 The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
87 Careful: FROGS Tree works only with less than 10 000 sequences!
88
89 .. image:: static/images/frogs_images/frogs_tree_otufile.png
90
91 **OTUs biom file**:
92
93 The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
94 This file can be obtained in particular with the FROGS pipeline.
95
96 .. class:: h3
97
98 Outputs
99
100 **Newick file** (tree.nwk):
101
102 The phylogenetic tree in Newick format (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
103
104 .. image:: static/images/frogs_images/nwk_treefile.png
105
106 **Html file** (summary.html):
107
108 The summary file describing which OTUs are contained or not in the phylogenetic tree.
109
110 .. class:: infomark page-header h2
111
112 **Contact**
113
114 Contacts: frogs@inra.fr
115
116 Repository: https://github.com/geraldinepascal/FROGS
117 website: http://frogs.toulouse.inra.fr/
118
119 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
120
121 </help>
122 <citations>
123 <citation type="doi">10.1093/bioinformatics/btx791</citation>
124 </citations>
125
126 </tool>