<?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.
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# 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_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="@TOOL_VERSION@+galaxy2">
	<description>Converts a FROGS BIOM in fully compatible BIOM.</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="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 '$output_blast_details'
	</command>
	<inputs>
		<!-- Files -->
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
	</inputs>
	<outputs>
		<data format="biom1" name="output_biom" label="${tool.name}: abundance.standard.biom" from_work_dir="abundance.biom"/>
		<data format="tabular" name="output_blast_details" label="${tool.name}: all_blast_details.tsv" from_work_dir="blast_details.tsv" />
	</outputs>
	<tests>
		<test>
			<param name="input_biom" value="references/09-normalisation.biom"/>
			<output name="output_biom" value="references/13-affiliation_std.biom" compare="sim_size" delta="0" />
			<output name="output_blast_details" value="references/13-affiliation_multihit.tsv" compare="diff" lines_diff="0" />
		</test>
	</tests>
	<help>

@HELP_LOGO@

.. 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 blast details 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 ambiguous blast details (format `BIOM &lt;http://biom-format.org/&gt;`_).

**Blast details 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 details in a second file, write a BIOM usable in every tools using BIOM and defined the consensus taxonomy provided by blast as main taxonomy.



@HELP_CONTACT@

	</help>

	<citations>
		<expand macro="citations" />
	</citations>
	
</tool>