<?xml version="1.0"?>
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# Copyright (C) 2015 INRA
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# This program is free software: you can redistribute it and/or modify
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# the Free Software Foundation, either version 3 of the License, or
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<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="2.0.0">
        <description>Normalize OTUs abundance.</description>
        <requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <!--stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio-->
	<command>
		normalisation.py 
		                       --input-biom $input_biom
		                       --input-fasta $input_fasta
		                       --num-reads $num_reads
		                       --output-biom $output_biom
		                       --output-fasta $output_fasta 
		                       --summary-file $summary_file 
	</command>
	<inputs>
		<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
		<param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
	</inputs>
	<outputs>
		<data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
		<data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
	</outputs>
        <tests>
                <test>
	                <param name="input_fasta" value="references/04-filters.fasta"/>
        	        <param name="input_biom" value="references/04-affiliation.biom"/>
                	<param name="num_reads" value="100"/>
	                <output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" />
                </test>
        </tests>
	<help>

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


.. class:: infomark page-header h2

What it does

This tool keeps, in each sample, the same number of elements by random sampling.

.. 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

**Sequence file** (normalised_seed.fasta):

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

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

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

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

 Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).


.. class:: infomark page-header h2

Advices

The number specified in "Number of reads" must be smaller than each total number of sequences by sample.


----

**Contact**

Contacts: frogs@inra.fr

Repository: https://github.com/geraldinepascal/FROGS

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

Depending on the help provided you can cite us in acknowledgements, references or both.
	</help>
	<citations>
		<citation type="doi">10.7287/peerj.preprints.386v1</citation>
	</citations> 
</tool>