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comparison affiliation_OTU.xml @ 0:76c750c5f0d1 draft default tip

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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_affiliation_OTU" name="FROGS Affiliation OTU" version="0.8.0">
19 <description>Step 4 in metagenomics analysis : Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</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 #set $reference_fasta_filename = str( $ref_file.fields.path )
29 affiliation_OTU.py
30 --reference "${reference_fasta_filename}"
31 --input-biom $biom_abundance
32 --input-fasta $fasta_sequences
33 --output-biom $biom_affiliation
34 --summary $summary
35 --nb-cpus $nb_cpu
36 --java-mem $mem
37 #if $rdp
38 --rdp
39 #end if
40 </command>
41 <inputs>
42 <!-- JOB Parameter -->
43 <param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param>
44 <param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>
45 <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">
46 <options from_data_table="frogs_db"></options>
47 <validator type="no_options" message="A built-in database is not available" />
48 </param>
49 <param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" />
50 <!-- Files -->
51 <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>
52 <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>
53 </inputs>
54 <outputs>
55 <data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" />
56 <data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>
57 </outputs>
58 <tests>
59 <test>
60 <param name="ref_file" value="db"/>
61 <param name="fasta_sequences" value="swarm.fasta"/>
62 <param name="biom_abundance" value="swarm.biom"/>
63 <output name="biom_affiliation" file="references/Blast_affiliation.biom"/>
64 <output name="summary" file="references/Blast_affiliation.html" compare="sim_size" delta="0" />
65 </test>
66 </tests>
67
68 <help>
69
70 .. image:: static/images/FROGS_logo.png
71 :height: 144
72 :width: 110
73
74
75 .. class:: infomark page-header h2
76
77 What it does
78
79 Add taxonomic affiliation in abundance file.
80
81
82 .. class:: infomark page-header h2
83
84 Inputs/outputs
85
86 .. class:: h3
87
88 Inputs
89
90 **Sequence file**:
91
92 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
93
94 **Abundance file**:
95
96 The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
97
98 .. class:: h3
99
100 Outputs
101
102 **Abundance file** (tax_affiliation.biom):
103
104 The abundance file with affiliation (format `BIOM &lt;http://biom-format.org/&gt;`_).
105
106 **Summary file** (report.html):
107
108 This file presents the number of sequences affiliated by blast, and the number of multi-affiliation (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
109
110 .. image:: static/images/FROGS_affiliation_summary.png
111 :height: 800
112 :width: 600
113
114
115 .. class:: infomark page-header h2
116
117 Reference database
118
119 The databases come from `SILVA &lt;http://www.arb-silva.de/&gt;`_ a comprehensive and quality checked rRNA database.
120
121 FROGS database(s) pre-process:
122
123 1. The non-redondant small sub-unit database is retrieved from SILVA.
124
125 2. This database is processed to keep only the taxonomy level: Domain - Phylum - Class - Order - Family - Genus - Species
126
127 3. The database is splitted in two databses: prokaryote and eukaryote.
128
129
130 .. class:: infomark page-header h2
131
132 How it works
133
134 .. csv-table::
135 :header: "Steps", "Description"
136 :widths: 5, 150
137 :class: table table-striped
138
139 "1", "`RDPClassifier &lt;https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html&gt;`_ is used with database to associate to each OTU a taxonomy and a bootstrap (example: *Bacteria;(1.0);Firmicutes;(1.0);Clostridia;(1.0);Clostridiales;(1.0);Clostridiaceae 1;(1.0);Clostridium sensu stricto;(1.0);*)."
140 "2", "`blastn+ &lt;http://blast.ncbi.nlm.nih.gov/&gt;`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score has reported."
141 "3", "For each OTU with several blastn+ results a consensus is determined on each taxonomic level. If all the taxa in a taxonomic rank are identical the taxon name is reported otherwise *Multi-affiliation* is reported. By example, if you have an OTU with two corresponding sequences, the first is a *Bacteria;Proteobacteria;Gamma Proteobacteria;Enterobacteriales*, the second is a *Bacteria;Proteobacteria;Beta Proteobacteria;Methylophilales*, the consensus will be *Bacteria;Proteobacteria;Multi-affiliation;Multi-affiliation*."
142
143
144 .. class:: infomark page-header h2
145
146 Advices
147
148 This tool can take large time. It is recommended to filter your abundance and your sequence file before this tool (see **FROGS Filters**).
149
150 As you can see the affiliation of each OTU is not human readable in outputed abundance file. We provide a tools to convert these BIOM file in tabulated file, see the **FROGS BIOM to TSV** tool.
151
152
153 ----
154
155 **Contact**
156
157 Contacts: frogs@inra.fr
158
159 Repository: https://github.com/geraldinepascal/FROGS
160
161 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
162
163 Depending on the help provided you can cite us in acknowledgements, references or both.
164 </help>
165 <citations>
166 <citation type="doi">10.1186/1471-2105-10-421</citation>
167 <citation type="doi">10.1128/AEM.00062-07</citation>
168 </citations>
169 </tool>