<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">

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

    <macros>
        <import>macros.xml</import>
        <import>macros_mixomics.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command detect_errors="aggressive"><![CDATA[

        @COMMAND_RSCRIPT@/mixomics_plotvar.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[

@HELP_AUTHORS@

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

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

This tool allows visualizing the variables of a omics dataset which are correlated with the variables
of the other omic datasets and the response variable in a correlation circle.

-----------------
Workflow position
-----------------

**Upstream tools**

======================= =================================== ========
Name                    Output file                         Format
======================= =================================== ========
mixOmics.block.splsda   mixomics_blocksplsda_output.RData   rdata
======================= =================================== ========

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

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

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

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

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

Plot legend

Cut-off


@HELP_MANUAL@

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

plotVar.pdf
    A pdf file with scatter plots for variables

    ]]></help>

    <expand macro="citations" />

</tool>