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mixomics_plotindiv.xml
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<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="0.3.0" 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)"
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="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 ([email protected])
---------------------------------------------------
.. 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>