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affiliations_stat.xml
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affiliations_stat.xml
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<?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.
#
# 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_affiliations_stat" name="FROGS Affiliations stat" version="3.1">
<description>Process some metrics on taxonomies.</description>
<requirements>
<requirement type="package" version="3.1.0">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/06-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/09-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_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 <http://biom-format.org/>`_). 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 <https://en.wikipedia.org/wiki/HTML>`_):
*-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample
.. image:: static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png
:height: 380
:width: 650
.. image:: static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png
:height: 380
:width: 550
.. image:: static/images/frogs_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_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_images/FROGS_affiliation_stat_alignment.png
:height: 380
:width: 650
----
**Contact**
Contacts: [email protected]
Repository: https://github.com/geraldinepascal/FROGS
website: http://frogs.toulouse.inra.fr/
Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
</help>
<citations>
<citation type="doi">10.1093/bioinformatics/btx791</citation>
</citations>
</tool>