<?xml version="1.0"?>
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# Copyright (C) 2015 INRA
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-->
<tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="1.1.0">
	<description>Process some metrics on taxonomies.</description>
        <requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio> 
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>
	<command>
		affiliations_stat.py 
		    --input-biom $biom
		    --output-file $summary_file
		    --rarefaction-ranks $rarefaction_ranks
		    #if $affiliation.affiliation_type == "FROGS_blast"
		        --taxonomic-ranks Domain Phylum Class Order Family Genus Species
		    	--multiple-tag "blast_affiliations"
		        --tax-consensus-tag "blast_taxonomy"
		        --identity-tag "perc_identity"
		        --coverage-tag "perc_query_coverage"
			#else if $affiliation.affiliation_type == "FROGS_rdp"
			    --taxonomic-ranks Domain Phylum Class Order Family Genus Species
				--taxonomy-tag "rdp_taxonomy"
				--bootstrap-tag "rdp_bootstrap"
			#else
				--taxonomic-ranks $affiliation.taxonomic_ranks
				--taxonomy-tag "$affiliation.taxonomy_tag"
				#if $affiliation.bootstrap_tag
					--bootstrap-tag "$affiliation.bootstrap_tag"
				#end if
				#if $affiliation.identity_tag and $affiliation.coverage_tag
					--identity-tag "$affiliation.identity_tag"
					--coverage-tag "$affiliation.coverage_tag"
				#end if
			#end if
	</command>
	<inputs>
		<!-- Files -->
		<param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" />
		<!-- Parameters -->
		<param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" />
		<conditional name="affiliation">
			<param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'.">
				<option value="FROGS_blast" selected="true">FROGS blast</option>
				<option value="FROGS_rdp">FROGS rdp</option>
				<option value="custom">Custom</option>
			</param>
			<when value="FROGS_blast"></when>
			<when value="FROGS_rdp"></when>
			<when value="custom">
				<param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" />
				<param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" />
				<param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" />
				<param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" />
				<param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" />
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
	</outputs>
	<tests>
		<test>
			<param name="biom" value="references/04-affiliation.biom" />
			<param name="rarefaction_ranks" value="Family Genus Species" />
			<conditional name="affiliation">
				<param name="affiliation_type" value="FROGS_blast" />
				<param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" />
				<param name="taxonomy_tag" value="blast_taxonomy" />
				<param name="identity_tag" value="perc_identity" />
				<param name="coverage_tag" value="perc_query_coverage" />
				<!-- pas de parametre dans le formulaire pour multiple-tag, uniquement une option dans la ligne de commande -->
			</conditional>
			<output name="summary_file" file="references/06-affiliationsStat.html" compare="sim_size" delta="0" />
			<!-- log-file option presente dans la ligne de commande dans le test.sh n'apparait pas du tout ici -->
		</test>
	</tests>
	<help>

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


.. class:: infomark page-header h2

What it does

FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and the quality of the affiliations.


.. class:: infomark page-header h2

Input/output

.. class:: h3

Input

**Abundance file**:
 
The abundance and affiliation of each OTUs in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_). This file can be produced by FROGS Affiliation OTU.

The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.

.. class:: h3

Output

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

 OTUs taxonomies and affiliations metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
 
  *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample
  
  .. image:: static/images/FROGS_affiliation_stat_taxonomies.png
    :height: 380
    :width: 650  

  .. image:: static/images/FROGS_affiliation_stat_rarefaction.png
    :height: 380
    :width: 550

  .. image:: static/images/FROGS_affiliation_stat_sunburst.png
    :height: 380
    :width: 430
  
  -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank

  .. image:: static/images/FROGS_affiliation_stat_bootstrap.png
    :height: 380
    :width: 650

  -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage

  .. image:: static/images/FROGS_affiliation_stat_alignment.png
    :height: 380
    :width: 650



----

**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">10.1093/bioinformatics/btx791</citation>
                <citation type="doi">10.1128/AEM.01043-13</citation>
                <citation type="doi">10.14806/ej.17.1.200</citation>
                <citation type="doi">10.1093/bioinformatics/btr507</citation>
        </citations>

</tool>