Mercurial > repos > ppericard > mixomics_blocksplsda
view mixomics_plotvar.xml @ 3:0a3c83f2197a draft
planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author | ppericard |
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date | Fri, 25 Oct 2019 07:10:59 -0400 |
parents | 655d1fbcd3e6 |
children | b0ab97ffc2a1 |
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<tool id="mixomics_plotvar" name="mixOmics plotVar" version="0.2.0" 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>