forked from geraldinepascal/FROGS-wrappers
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtree.xml
137 lines (108 loc) · 5.52 KB
/
tree.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
<?xml version="1.0"?>
<!--
# Copyright (C) 2017 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGS_Tree" name="FROGS Tree" version="1.0.0">
<description>Reconstruction of phylogenetic tree </description>
<requirements>
<requirement type="package" version="2.0.1">frogs</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
</stdio>
<command>tree.py
--input-otu $input_otu
#if $template.fileTemplate
--template-pynast ${template.template_pynast}
#end if
--biomfile $biomfile
--nb-cpus $nb_cpus
--out-tree $out_tree
--html $html
</command>
<inputs>
<!-- Files -->
<param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
<validator type="empty_field" message="This parameter is required." />
</param>
<conditional name="template">
<param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" />
<when value="false"></when>
<when value="true">
<param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" />
</when>
</conditional>
<param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
<validator type="empty_field" message="This parameter is required." />
</param>
<!-- Parameter -->
<param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />
</inputs>
<outputs>
<data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
<data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
</outputs>
<tests>
<test>
<param name="input_otu" value="references/04-filters.fasta"/>
<conditional name="template">
<param name="fileTemplate" value="false"/>
</conditional>
<param name="biomfile" value="references/04-affiliation.biom"/>
<output name="out_tree" value="references/10b-tree.nwk"/>
</test>
</tests>
<help>
.. image:: static/images/FROGS_logo.png
:height: 144
:width: 110
.. class:: infomark page-header h2
What it does
Creation of a multiple alignment of OTUs with `PyNAST <http://biocore.github.io/pynast/>`_ (if you have an alignment template file) or with `Mafft <http://mafft.cbrc.jp/alignment/software>`_ (if you have not an aligned template file).
And creation of a phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_.
.. class:: infomark page-header h2
Inputs/Outputs
.. class:: h3
Input
**OTUs fasta file**:
The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_).
Careful: FROGS Tree works only with less than 10 000 sequences!
.. image:: static/images/frogs_tree_otufile.png
**(optional) Template alignment file**:
A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_).
.. image:: static/images/frogs_tree_templatefile.png
**OTUs biom file**:
The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_).
This file can be obtained in particular with the FROGS pipeline.
.. class:: h3
Outputs
**Newick file** (tree.nwk):
The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_).
.. image:: static/images/nwk_treefile.png
**Html file** (summary.html):
The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML <https://en.wikipedia.org/wiki/HTML>`_).
.. class:: infomark page-header h2
**Contact**
Contacts: frogs@inra.fr
Repository: https://github.com/geraldinepascal/FROGS
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
Depending on the help provided you can cite us in acknowledgements, references or both.
</help>
<citations>
<citation type="doi">10.7287/peerj.preprints.386v1</citation>
</citations>
</tool>