view affiliation_OTU.xml @ 0:59bc96331073 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647

<?xml version="1.0"?>
<!--
# Copyright (C) 2015 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-->
<tool id="FROGS_affiliation_OTU" name="FROGS Affiliation OTU" version="3.1">
	<description>Taxonomic affiliation of each OTU's seed by RDPtools and BLAST</description>
 	<requirements>
                <requirement type="package" version="3.1.0">frogs</requirement>
        </requirements>
     	<stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		#set $reference_filename = str( $ref_file.fields.path )
		affiliation_OTU.py 
		                       --reference "${reference_filename}"
		                       --input-biom $biom_abundance 
		                       --input-fasta $fasta_sequences
		                       --output-biom $biom_affiliation 
		                       --summary $summary 
		                       --nb-cpus \${GALAXY_SLOTS:-1}
		                       --java-mem $mem 
		                       #if $rdp
		                       		--rdp
		                       	#end if
	</command>
	<inputs>
		<!-- JOB Parameter -->
		<param name="mem" type="hidden" label="Memory allocation" help="The number of Go to allocation for java" value="20"></param>
		<!-- Database Choice -->
		<param name="ref_file" type="select" label="Using reference database" help="Select reference from the list">
	       		<options from_data_table="frogs_db"></options>
			<validator type="no_options" message="A built-in database is not available" />
		</param> 
   		<param name="rdp" type="boolean" label="Also perform RDP assignation?" help="Taxonomy affiliation will be perform thanks to Blast. This option allow you to perform it also with RDP classifier (default No)" />
	        <!-- Files -->
	        <param format="fasta" name="fasta_sequences" type="data" label="OTU seed sequence" help="OTU sequences (format: fasta)."/>
	        <param format="biom1" name="biom_abundance" type="data" label="Abundance file" help="OTU abundances (format: BIOM)."/>
	</inputs>
	<outputs>
		<data format="biom1" name="biom_affiliation" label="${tool.name}: affiliation.biom" from_work_dir="affiliation.biom" />
		<data format="html" name="summary" label="${tool.name}: report.html" from_work_dir="report.html"/>
	</outputs>
        <tests>
            <test>
                <param name="ref_file" value="ITS1_test"/>
                <param name="fasta_sequences" value="references/04-filters.fasta"/>
                <param name="biom_abundance" value="references/04-filters.biom"/>
                <!-- <param name="fasta_sequences" value="swarm.fasta"/>
                <param name="biom_abundance" value="swarm.biom"/> -->
                <output name="biom_affiliation" file="references/06-affiliation.biom"/>
                <output name="summary" file="references/06-affiliation.html" compare="sim_size" delta="0" />
            </test>
        </tests>

  	<help>

.. image:: static/images/frogs_images/FROGS_logo.png 
   :height: 144
   :width: 110


.. class:: infomark page-header h2

What it does

Add taxonomic affiliation in abundance file.


.. class:: infomark page-header h2

Inputs/outputs

.. class:: h3

Inputs

**Sequence file**:

The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).

**Abundance file**:
 
The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).

.. class:: h3

Outputs

**Abundance file** (tax_affiliation.biom):

 The abundance file with affiliation (format `BIOM &lt;http://biom-format.org/&gt;`_).

**Summary file** (report.html):

 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;`_).
 
 .. image:: static/images/frogs_images/FROGS_affiliation_summary.png 
    :height: 800
    :width: 600


.. class:: infomark page-header h2

Reference database

All the databases we format (on demand) for RDPClassifier and NCBI Blast+ are inventoried here: http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/readme.txt

.. class:: infomark page-header h2

How it works

.. csv-table:: 
   :header: "Steps", "Description"
   :widths: 5, 150
   :class: table table-striped

   "1", "`RDPClassifier &lt;https://rdp.cme.msu.edu/tutorials/classifier/RDPtutorial_RDP_classifier.html&gt;`_ may be 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);*)."
   "2", "`blastn+ &lt;http://blast.ncbi.nlm.nih.gov/&gt;`_ or `needlall &lt;http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html&gt;`_ is used to find alignment between each OTU and the database. Only the bests hits with the same score are reported. blastn+ is used for merged read pair, and needall is used for artificially combined sequence. For each alignment returned, several metrics are computed: identity percentage, coverage percentage, and alignment length"
   "3", "For each OTU with several blastn+/needlall alignment 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*."

.. class:: infomark page-header h2

Alignment metrics details on identity percentage calculation

With classicala %id computation method, we will obtain for overlapped amplicon sequence and for artificially combined amplicon sequence :

* **Case 1: a sequencing of overlapping sequences i.e. 16S V3-V4 amplicon MiSeq sequencing**

.. image:: static/images/frogs_images/FROGS_affiliation_overlapped_percent_id.png
    :height: 325
    :width: 807

* **Case 2 : a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**

.. image:: static/images/frogs_images/FROGS_affiliation_combined_percent_id.png
    :height: 310
    :width: 887

* **Finally, how percentage identity is computed ?**

With the classical method of %id calculation, filtering on %id will systematically removed “FROGS combined” OTUs. So, we proposed to replace the classical %id by a %id computed on the sequenced bases only.

.. image:: static/images/frogs_images/FROGS_affiliation_percent_id_formula.png
    :height: 36
    :width: 637

For the precedent use cases we will obtain:

* Case 1: 16S V3V4 overlapped sequence
	% sequenced bases identity = 400 matches / 400 bp = 100%

* Case 2: very large ITS1 “FROGS combined” shorter than the real sequence
	% sequenced bases identity = (250 + 250 ) / (600 - 100) = 100%

This calculation allows to return 100% of identity on sequenced bases for “FROGS combined” shorter or longer than reality in case of perfect sequencing, and a smaller percentage of identity in the case of small overlap repeat kept in FROGS combined sequence. 

.. class:: infomark page-header h2


Advices

This tool can take large time. It is recommended to filter your abundance and your sequence file before this tool (see **FROGS Filters**).

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.


----

**Contact**

Contacts: [e-mail]

Repository: https://github.com/geraldinepascal/FROGS
website: http://frogs.toulouse.inra.fr/

Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*

	</help>
	<citations>
		<citation type="doi">10.1093/bioinformatics/btx791</citation>
	</citations>

</tool>