<?xml version="1.0"?>
<!--
# 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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# This program is distributed in the hope that it will be useful,
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-->
<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="1.1.0">
	<description>Converts a FROGS BIOM in fully compatible BIOM.</description>
 	<requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		biom_to_stdBiom.py 
		                --input-biom $input_biom
		                --output-biom $output_biom
		                --output-metadata $output_metadata 
	</command>
	<inputs>
		<!-- Files -->
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
	</inputs>
	<outputs>
		<data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/>
		<data format="tabular" name="output_metadata" label="${tool.name}: blast_metadata.tsv" from_work_dir="blast_metadata.tsv" />
	</outputs>
	<tests>
		<test>
			<param name="input_biom" value="references/04-affiliation.biom"/>
			<output name="output_biom" value="references/08-affiliation_std.biom"/>
			<output name="output_metadata" value="references/08-affiliation_multihit.tsv"/>
		</test>
	</tests>
	<help>

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


.. class:: infomark page-header h2

What it does

Converts a BIOM generated by FROGS in generic BIOM.

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.

.. class:: h3

Inputs

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

.. class:: h3

Outputs

**Abundance file**:

 The abundance without the incompatible metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).

**Blast metadata file**:

 The details for each alignment on clusters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).


.. class:: infomark page-header h2

How it works

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.



----

**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., 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

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>