<tool id="mixomics_plotvar" name="mixOmics plotVar" version="1.0" profile="16.04" workflow_compatible="true">

    <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>

    <requirements>
        <requirement type="package" version="6.12">bioconductor-mixomics</requirement>
        <requirement type="package" version="2.0">r-argparse</requirement>
    </requirements>

    <stdio>
        <!-- <exit_code range="1:" level="fatal" /> -->
    </stdio>

    <command detect_errors="aggressive">
        <![CDATA[
        Rscript
        ${__tool_directory__}/mixomics_plotvar_script.R
        --input_rdata $input_rdata
        $adv.legend
        --cutoff $adv.cutoff
        --output_pdf $output_pdf
        ]]>
    </command>

    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
               help="This is the RData output file from the block.splsda function." />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
                   label="Plot legend" />
            <param name="cutoff" type="float" value="0" min="0" max="1"
                   label="Cut-off"
                   help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." />
        </section>
    </inputs>

    <outputs>
        <data name="output_pdf" format="pdf" label="plotVar.pdf" />
    </outputs>

    <tests>
        <test>
            <param name="input_rdata" value="out_rdata.rdata" />
            <output name="output_pdf" value="out_plotVar.pdf" />
        </test>
    </tests>

    <help>
        <![CDATA[
.. class:: infomark

**Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)

---------------------------------------------------

.. class:: infomark

**Please cite**

Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752

---------------------------------------------------

================
mixOmics plotVar
================

-----------
Description
-----------

The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.

-----------
Input files
-----------

+-------------------------------+------------+
| Parameter : num + label       |   Format   |
+===============================+============+
| 1 : Rdata block.splsda output |   Rdata    |
+-------------------------------+------------+

----------
Parameters
----------

Advanced options:
=================

Plot legend

Cut-off

------------
Output files
------------

plotIndiv.pdf
    A pdf file with scatter plots for individuals

        ]]>
    </help>

    <citations>
        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
    </citations>

</tool>