<?xml version="1.0"?>
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# Copyright (C) 2017 INRA
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# This program is free software: you can redistribute it and/or modify
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<tool name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="1.0.0">
	<description>from 3 files: biomfile, samplefile, treefile </description>
 	<requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio>
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>r_import_data.py --biomfile $biomfile
                                                   #if $samplefile
                                                      --samplefile $samplefile 
                                                   #end if
                                                      --treefile $treefile 
                                                      --ranks "$ranks"
	                                               #if $normalization
                                                      --normalization
                                                   #end if
                                                      --html $html 
                                                      --rdata $data
	</command>
    <inputs>
		<!-- Files -->
		<param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the  OTU informations (format: biom1)." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
        
		<param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
            <validator type="empty_field" message="This parameter is required." />                
        </param>
        
		<param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
        
        <!-- Parameters -->
		<param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space."  value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
		<param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> 
	</inputs>
	<outputs>
		<data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
		<data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
	</outputs>
	<tests>
		<test>
			<param name="biomfile" value="references/chaillou.biom"/>
			<param name="samplefile" value="references/sample_metadata.tsv"/>
			<param name="treefile" value="references/tree.nwk"/>
			<output name="data" value="references/11-phylo_import.Rdata"/>
		</test>
	</tests>

	<help>

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

.. class:: infomark page-header h2

What it does

Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ object.

.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**OTU biom file**:

The OTU biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
This file is the result of FROGS BIOM to std BIOM.
The example of biom file: 

  .. image:: static/images/biomfile.png 
     :height: 30
     :width: 733 

**Newick file** (tree.nwk):

Newick file (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_) is the result of FROGS Tree:

  .. image:: static/images/nwk_treefile.png

**Sample file**:
The file contains the conditions of experiment with sample ID in the first column:
  
  .. image:: static/images/phyloseq_samplefile.png 
     :height: 115
     :width: 369
      
.. class:: h3

Output

**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The summary of phyloseq object.
  
  .. image:: static/images/phyloseq_import_data_html.png 
 
**Data file** (format rdata): The informations of data in one phyloseq object.


.. class:: infomark page-header h2

**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>