view phyloseq_clustering.xml @ 0:834843ebe569 draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.2 commit 6150f59723cf8b0d3c0a2e35208078473f0ec5cf"

<?xml version="1.0"?>
<!--
# Copyright (C) 2017 INRA
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<tool name="FROGSSTAT Phyloseq Sample Clustering" id="FROGSSTAT_Phyloseq_Sample_Clustering" version="3.2.2">
	<description>of samples using different linkage methods</description>
        <requirements>
            <requirement type="package" version="3.2.2">frogs</requirement>
            <requirement type="package" version="3.6.3">r-base</requirement>
            <requirement type="package" version="3.6">r-essentials</requirement>
            <requirement type="package" version="1.30.0">bioconductor-phyloseq</requirement>
        </requirements>
	<stdio>
		<exit_code range="1:" />
		<exit_code range=":-1" />
	</stdio>
	<command>phyloseq_clustering.py 
                                   --html $html 
                                   --rdata $data 
                                   --varExp $varExp 
                                   --distance-matrix $method
	</command>
    <inputs>
		<!-- Files -->
	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This is the result of FROGS Phyloseq Import Data tool." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
        <param name="method" format="tabular" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool." optional="false">
            <validator type="empty_field" message="This parameter is required." />
        </param>
		<!-- Parameters -->	
		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
            <validator type="empty_field" message="This parameter is required." />
        </param>	
	</inputs>
	<outputs>
		<data format="html" name="html" label="${tool.name}: clustering.nb.html" from_work_dir="clustering.nb.html"/>
	</outputs>
	<tests>
		<test>
			<param name="data" value="references/16-phylo_import.Rdata"/>
			<param name="varExp" value="EnvType"/>
			<param name="method" value="references/unifrac.tsv"/>
      <output name="html">
        <assert_contents>
          <has_text text='FROGS Phyloseq: Sample clustering using different linkage method' />
          <has_text text='Phyloseq 1.30.0' />
        </assert_contents>
      </output>
		</test>
	</tests>
	<help>
		
.. image:: static/images/FROGS_logo.png 
   :height: 144
   :width: 110

.. class:: infomark page-header h2

What it does

Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool contructs the clustering plot for cluster analysis with different linkage methods.


.. class:: infomark page-header h2

Inputs/Outputs

.. class:: h3

Input

**data file** (format RData):
The informations of data in one phyloseq object.
This is the result of FROGS Phyloseq Import Data tool.

**distance file** (format tabular):
The data file containing beta diversity distance matrix.
This file is the result of FROGS Phyloseq Beta Diversity tool. 

.. class:: h3

Output

**html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):

.. container:: row

 .. image:: static/images/FROGS_Phyloseq_clustering_ward.png 
   :height: 576
   :width: 768

.. class:: infomark page-header h2

**Contact**

Contacts: [e-mail]

Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers

Website: http://frogs.toulouse.inrae.fr/

Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. &lt;https://doi.org/10.1093/bioinformatics/btx791&gt;`_

	</help>
</tool>