view cluster_stats.xml @ 8:0966b9635d76 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 43fa7e46c98b5d5d7915f86524d4c0c4f501d782

<tool id="FROGS_cluster_stats" name="FROGS_Cluster_Stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="GPL-2.0-only" profile="20.05">
	<description>Process some metrics on clusters </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
	cluster_stats.py
		--input-biom '$biom'
		--output-file '$summary_file'
	</command>
	<inputs>
		<param format="biom1" name="biom" type="data" label="Abundance file" help="Clusters abundance (format: BIOM)"/>
	</inputs>
	<outputs>
		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="summary.html"/>
	</outputs>
	<tests>
		<test>
			<param name="biom" value="references/09-normalisation.biom"/>
			<output name="summary_file" value="references/10-clustersStat.html" compare="diff" lines_diff="0"/>
		</test>
	</tests>
	<help>

@HELP_LOGO@

.. class:: infomark page-header h2

What it does

FROGS Cluster stats computes several metrics and generates a HTML file describing clusters based on abundances, samples, ...


.. class:: infomark page-header h2

Input/output

.. class:: h3

Input

**Abundance file**:

The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).

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

.. class:: h3

Output

**Report file** (report.html):

 *Cluster distribution* : describes the sizes distribution of all clusters thanks to boxplots and tables

 .. image:: FROGS_cluster_stats_clusterDistrib1.png
    :height: 1180
    :width: 900

 *Sequence distribution* : describes the sequences distribution among clusters

 .. image:: FROGS_cluster_stats_seq_dist.png

 *Sample distribution* : describes clusters distribution among samples and gives an `hierarchical clustering &lt;http://en.wikipedia.org/wiki/Hierarchical_clustering&gt;`_ on samples abundance profile (distance method = `braycurtis &lt;http://fr.wikipedia.org/wiki/Distance_de_Bray-Curtis&gt;`_, linkage method = average)

 .. image:: FROGS_cluster_stats_sample_dist1.png
    :height: 400
    :width: 700

 .. image:: FROGS_cluster_stats_sample_dist2.png
    :height: 350
    :width: 610

.. class:: infomark page-header h2

Advices

This is a very usefull tool to see the evolution of the clusters. Do not hesitate to run this tool after each FROGS step beginning at the clustering step.



@HELP_CONTACT@

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