Mercurial > repos > frogs > frogs_2_0_0
comparison tree.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author | frogs |
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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 id="FROGS_Tree" name="FROGS Tree" version="1.0.0"> | |
19 <description>Reconstruction of phylogenetic tree </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>tree.py | |
28 --input-otu $input_otu | |
29 #if $template.fileTemplate | |
30 --template-pynast ${template.template_pynast} | |
31 #end if | |
32 --biomfile $biomfile | |
33 --nb-cpus $nb_cpus | |
34 --out-tree $out_tree | |
35 --html $html | |
36 </command> | |
37 <inputs> | |
38 <!-- Files --> | |
39 <param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false"> | |
40 <validator type="empty_field" message="This parameter is required." /> | |
41 </param> | |
42 <conditional name="template"> | |
43 <param name="fileTemplate" type="boolean" label="Do you have the template alignment file ?" help="If yes, precise the template multi-alignment file." optional="false" /> | |
44 <when value="false"></when> | |
45 <when value="true"> | |
46 <param format="fasta" name="template_pynast" type="data" label="Template alignment file" help="Template multi-alignment file (format: fasta)." optional="false" /> | |
47 </when> | |
48 </conditional> | |
49 <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false"> | |
50 <validator type="empty_field" message="This parameter is required." /> | |
51 </param> | |
52 <!-- Parameter --> | |
53 <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" /> | |
54 </inputs> | |
55 <outputs> | |
56 <data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/> | |
57 <data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/> | |
58 </outputs> | |
59 <tests> | |
60 <test> | |
61 <param name="input_otu" value="references/04-filters.fasta"/> | |
62 <conditional name="template"> | |
63 <param name="fileTemplate" value="false"/> | |
64 </conditional> | |
65 <param name="biomfile" value="references/04-affiliation.biom"/> | |
66 <output name="out_tree" value="references/10b-tree.nwk"/> | |
67 </test> | |
68 </tests> | |
69 <help> | |
70 .. image:: static/images/FROGS_logo.png | |
71 :height: 144 | |
72 :width: 110 | |
73 | |
74 .. class:: infomark page-header h2 | |
75 | |
76 What it does | |
77 | |
78 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). | |
79 And creation of a phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_. | |
80 | |
81 .. class:: infomark page-header h2 | |
82 | |
83 Inputs/Outputs | |
84 | |
85 .. class:: h3 | |
86 | |
87 Input | |
88 | |
89 **OTUs fasta file**: | |
90 | |
91 The OTUs sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). | |
92 Careful: FROGS Tree works only with less than 10 000 sequences! | |
93 | |
94 .. image:: static/images/frogs_tree_otufile.png | |
95 | |
96 **(optional) Template alignment file**: | |
97 | |
98 A pre-aligned database of sequences (the “template” sequence) (format `multiple alignement <https://en.wikipedia.org/wiki/Multiple_sequence_alignment>`_). | |
99 | |
100 .. image:: static/images/frogs_tree_templatefile.png | |
101 | |
102 **OTUs biom file**: | |
103 | |
104 The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). | |
105 This file can be obtained in particular with the FROGS pipeline. | |
106 | |
107 .. class:: h3 | |
108 | |
109 Outputs | |
110 | |
111 **Newick file** (tree.nwk): | |
112 | |
113 The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). | |
114 | |
115 .. image:: static/images/nwk_treefile.png | |
116 | |
117 **Html file** (summary.html): | |
118 | |
119 The summary file describing which OTUs are contained or not in the phylogenetic tree (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). | |
120 | |
121 .. class:: infomark page-header h2 | |
122 | |
123 **Contact** | |
124 | |
125 Contacts: frogs@inra.fr | |
126 | |
127 Repository: https://github.com/geraldinepascal/FROGS | |
128 | |
129 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 | |
130 | |
131 Depending on the help provided you can cite us in acknowledgements, references or both. | |
132 | |
133 </help> | |
134 <citations> | |
135 <citation type="doi">10.7287/peerj.preprints.386v1</citation> | |
136 </citations> | |
137 </tool> |