<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="0.1.0" profile="16.04" workflow_compatible="true">

    <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description>
    
    <requirements>
        <requirement type="package" version="6.8">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_plotindiv_script.R
        --input_rdata $input_rdata
        $adv.legend
        $adv.ellipse
        --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)"/>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" label="Plot legend"/>
            <param name="ellipse" type="boolean" checked="true" truevalue="--ellipse" falsevalue="" label="Plot ellipse plots"/>
        </section>
    </inputs>

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

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

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

The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets.
Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA).

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

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

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

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

Plot legend

Plot ellipse plots

------------
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>