view phyloseq_clustering.xml @ 3:8edcbafb3b4e draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2024a13846ea6f9bd94ae62e3b2a5a3aba8cd304-dirty"

<?xml version="1.0"?>
<!--
# Copyright (C) 2017 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="FROGSSTAT_Phyloseq_Sample_Clustering" name="FROGSSTAT Phyloseq Sample Clustering" version="@TOOL_VERSION@+galaxy2">
	<description>of samples using different linkage methods</description>

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

    <expand macro="requirements_phyloseq" />

	<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" file="references/21-phylo_clustering.nb.html" compare="diff" lines_diff="0"/> -->
      		<output name="html">
      			<assert_contents>
                    <has_text text='FROGS Phyloseq: Sample clustering using different linkage method (version 3.2.3)' />
                    <has_text text='Phyloseq 1.34.0' />
                    <has_text text='Ward D2' />
                    <has_text text='Complete' />
                    <has_text text='Single' />
                    <has_text text='img src=' />
                </assert_contents>
            </output>
		</test>
	</tests>
	<help>

@HELP_LOGO@

.. 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

@HELP_CONTACT@

	</help>

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