view mixomics_plotvar.xml @ 1:6595c17673cb draft

planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
author ppericard
date Wed, 12 Jun 2019 11:22:33 -0400
parents bea08702ed51
children 655d1fbcd3e6
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<tool id="mixomics_plotvar" name="mixOmics plotVar" version="0.1.0" 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="6.8">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_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)"/>
        <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" />
        </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>