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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_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="1.1.0">
19 <description>Converts a FROGS BIOM in fully compatible BIOM.</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 biom_to_stdBiom.py
29 --input-biom $input_biom
30 --output-biom $output_biom
31 --output-metadata $output_metadata
32 </command>
33 <inputs>
34 <!-- Files -->
35 <param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
36 </inputs>
37 <outputs>
38 <data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/>
39 <data format="tabular" name="output_metadata" label="${tool.name}: blast_metadata.tsv" from_work_dir="blast_metadata.tsv" />
40 </outputs>
41 <tests>
42 <test>
43 <param name="input_biom" value="references/04-affiliation.biom"/>
44 <output name="output_biom" value="references/08-affiliation_std.biom"/>
45 <output name="output_metadata" value="references/08-affiliation_multihit.tsv"/>
46 </test>
47 </tests>
48 <help>
49
50 .. image:: static/images/FROGS_logo.png
51 :height: 144
52 :width: 110
53
54
55 .. class:: infomark page-header h2
56
57 What it does
58
59 Converts a BIOM generated by FROGS in generic BIOM.
60
61 The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the problematic metadata in a second file and writes a BIOM usable in every tools using BIOM.
62
63 .. class:: h3
64
65 Inputs
66
67 **Abundance file**:
68
69 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
70
71 .. class:: h3
72
73 Outputs
74
75 **Abundance file**:
76
77 The abundance without the incompatible metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
78
79 **Blast metadata file**:
80
81 The details for each alignment on clusters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
82
83
84 .. class:: infomark page-header h2
85
86 How it works
87
88 FROGS BIOM to std BIOM extracts the blast alignment metadata in a second file, write a BIOM usable in every tools using BIOM and defined the taxonomy provided by blast as main taxonomy.
89
90
91
92 ----
93
94 **Contact**
95
96 Contacts: frogs@inra.fr
97
98 Repository: https://github.com/geraldinepascal/FROGS
99
100 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
101
102 Depending on the help provided you can cite us in acknowledgements, references or both.
103 </help>
104 <citations>
105 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
106 </citations>
107 </tool>