<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy1" 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_LOG_EXIT@

    ]]></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
-----------

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.

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