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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"?>
2 <!--
3 # Copyright (C) 2015 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_normalisation" name="FROGS Abundance normalisation" version="2.0.0">
19 <description>Normalize OTUs abundance.</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>
28 normalisation.py
29 --input-biom $input_biom
30 --input-fasta $input_fasta
31 --num-reads $num_reads
32 --output-biom $output_biom
33 --output-fasta $output_fasta
34 --summary-file $summary_file
35 </command>
36 <inputs>
37 <param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
38 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
39 <param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
40 </inputs>
41 <outputs>
42 <data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
43 <data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
44 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
45 </outputs>
46 <tests>
47 <test>
48 <param name="input_fasta" value="references/04-filters.fasta"/>
49 <param name="input_biom" value="references/04-affiliation.biom"/>
50 <param name="num_reads" value="100"/>
51 <output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" />
52 </test>
53 </tests>
54 <help>
55
56 .. image:: static/images/FROGS_logo.png
57 :height: 144
58 :width: 110
59
60
61 .. class:: infomark page-header h2
62
63 What it does
64
65 This tool keeps, in each sample, the same number of elements by random sampling.
66
67 .. class:: infomark page-header h2
68
69 Inputs/outputs
70
71 .. class:: h3
72
73 Inputs
74
75 **Sequence file**:
76
77 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
78
79 **Abundance file**:
80
81 The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
82
83 .. class:: h3
84
85 Outputs
86
87 **Sequence file** (normalised_seed.fasta):
88
89 The normalised sequences file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
90
91 **Abundance file** (normalised_abundance.biom):
92
93 The normalised abundance file (format `BIOM &lt;http://biom-format.org/&gt;`_).
94
95 **Summary file** (report.html):
96
97 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
98
99
100 .. class:: infomark page-header h2
101
102 Advices
103
104 The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
105
106
107 ----
108
109 **Contact**
110
111 Contacts: frogs@inra.fr
112
113 Repository: https://github.com/geraldinepascal/FROGS
114
115 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
116
117 Depending on the help provided you can cite us in acknowledgements, references or both.
118 </help>
119 <citations>
120 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
121 </citations>
122 </tool>