<tool id="ctb_mds_plot" name="MDS Scatter Plot" version="0.1">
    <description>of molecule similarity</description>
    <requirements>
        <requirement type="package" version="0.13.1">scikit_learn</requirement>
        <requirement type="package" version="1.2.1">matplotlib</requirement>
    </requirements>
    <command interpreter='python'>
        mds_plot.py
            -i $infile
            --oformat $oformat
            -o $outfile
    </command>
    <inputs>
        <param name="infile" type="data" format="binary" label="Similarity Matrix"/>
        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
            <option value='png'>PNG</option>
            <option value='svg'>SVG</option>
        </param>
    </inputs>
    <outputs>
        <data type="data" format="png" name="outfile" label="${tool.name} on ${on_string}"></data>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="tabular" value="sm.dat" />
            <output ftype="png" name="outfile" file='mds_plot_on_sm_dat.png' />
        </test>
    </tests>
    <help>

**Note**. You need an NxN similarity matrix as input. Use the NxN Clustering tool to generate one.

**What it does**

Scatter plot of similarity matrix after embeding in 2D coordinates using Multidimensional Scaling (MDS).

-----

**Example**

* input::
    Similarity Matrix

* output::

	Scatter plot

.. image:: $PATH_TO_IMAGES/mds_plot.png

    </help>

</tool>