view phyloseq_clustering.xml @ 4:445b04a65ed8 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 7519abe5ffbbe6144efd0da6b41de08198510cc3

<tool id="FROGSSTAT_Phyloseq_Sample_Clustering" name="FROGSSTAT Phyloseq Sample Clustering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
	<description>of samples using different linkage methods</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_phyloseq" />
    <command detect_errors="exit_code">
    phyloseq_clustering.py
        --html '$html'
        --rdata '$data'
        --varExp '$varExp'
        --distance-matrix '$distance_matrix'
	</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."/>
        <param argument="--distance-matrix" format="tsv" type="data" label="The beta diversity distance matrix file" help="This file is the result of FROGS Phyloseq Beta Diversity tool."/>
		<!-- Parameters -->
		<param argument="--varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse.">
            <expand macro="sanitizer_validator"/>
        </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="distance_matrix" 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 4.0.0)' />
                    <has_text text='Phyloseq 1.38.0' />
                    <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:: FROGS_Phyloseq_clustering_ward.png
   :height: 576
   :width: 768

.. class:: infomark page-header h2

@HELP_CONTACT@

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