Mercurial > repos > frogs > frogs_3_1_0

comparison biom_to_tsv.xml @ 0:59bc96331073 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:59bc96331073
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_tsv" name="FROGS BIOM to TSV" version="3.1">
19 <description>Converts a BIOM file in TSV file.</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>
28 biom_to_tsv.py
29 --input-biom $biom_file
30 #if $sequence_file
31 --input-fasta $sequence_file
32 #end if
33 --output-tsv $tsv_file
34 #if $extract_multi_align
35 --output-multi-affi $multi_affi_file
36 #end if
37 </command>
38 <inputs>
39 <!-- Files -->
40 <param format="biom1" name="biom_file" type="data" label="Abundance file" help="The BIOM file to convert (format: BIOM)." optional="false" />
41 <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta). If you use this option the sequences will be add in TSV." optional="true" />
42 <!-- Parameters -->
43 <param name="extract_multi_align" type="boolean" label="Extract multi-alignments" help="If you have used FROGS affiliation on your data, you can extract information about multiple alignements in a second TSV." checked="true"/>
44 </inputs>
45 <outputs>
46 <data format="tabular" name="tsv_file" label="${tool.name}: abundance.tsv" from_work_dir="abundance.tsv"/>
47 <data format="tabular" name="multi_affi_file" label="${tool.name}: multi_hits.tsv" from_work_dir="multi_hits.tsv" >
48 <filter>extract_multi_align</filter>
49 </data>
50 </outputs>
51 <tests>
52 <test>
53 <param name="biom_file" value="references/06-affiliation.biom"/>
54 <param name="sequence_file" value="references/04-filters.fasta"/>
55 <param name="extract_multi_align" value="true"/>
56 <output name="tsv_file" value="references/10-biom2tsv.tsv"/>
57 <output name="multi_affi_file" value="references/10-biom2tsv-affiliation_multihit.tsv"/>
58 </test>
59 </tests>
60 <help>
61
62 .. image:: static/images/frogs_images/FROGS_logo.png
63 :height: 144
64 :width: 110
65
66
67 .. class:: infomark page-header h2
68
69 What it does
70
71 Converts a BIOM file in TSV file.
72
73 .. class:: h3
74
75 Inputs
76
77 **Abundance file**:
78
79 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
80
81 **Sequence file [optional]**:
82
83 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
84
85 .. class:: h3
86
87 Outputs
88
89 **Abundance file**:
90
91 The abundance of each cluster in each sample and theirs metadata (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
92
93 If you add the sequences file, this information is added for each cluster.
94
95 **Multiple affiliation file**:
96
97 If you have used *FROGS affiliation* on your data, each OTU can have several affiliations: several alignments with same score on reference database. The multiple affiliation file contains details on these possibles affiliations (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
98
99
100 .. class:: infomark page-header h2
101
102 How it works
103
104 FROGS Biom to Tsv will search if any metadata are available, and the OTU sequence if fasta file is precised. Then it will extract the OTU name, sum the abundance, and extract the detailed abundance for each sample. Finally it will write all these fields separated by tabulation in the TSV file.
105
106
107 .. class:: infomark page-header h2
108
109 Advices
110
111 This output tsv file is easily readable in any spreadsheet software. Be aware that these software have a number of line limit (1 048 576 for Excel and LibreOffice calc ate least). If you have more OTU, use **FROGS Filters** to extract for example the most abundant OTU before converting your BIOM abundance table in TSV file.
112
113
114 ----
115
116 **Contact**
117
118 Contacts: frogs@inra.fr
119
120 Repository: https://github.com/geraldinepascal/FROGS
121 website: http://frogs.toulouse.inra.fr/
122
123 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
124
125 </help>
126 <citations>
127 <citation type="doi">10.1093/bioinformatics/btx791</citation>
128 </citations>
129
130 </tool>