--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,661 @@
+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
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+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published
+    by the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<https://www.gnu.org/licenses/>.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,2 @@
+# galaxy-mixomics-blocksplsda
+Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_blocksplsda.xml	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,224 @@
+<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.1.0" profile="16.04" workflow_compatible="true">
+
+    <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</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[
+        mkdir outdir
+        && Rscript
+        ${__tool_directory__}/mixomics_blocksplsda_script.R
+        #for $b in $blocks
+            --block
+            #if $b.block_name
+                ${b.block_name}
+            #else
+                ${b.data_matrix.name}
+            #end if
+            ${b.keep}
+            ${b.data_matrix}
+            ${b.variable_metadata}
+        #end for
+        --sample_metadata_in ${sample_metadata_in}
+        --sample_description_col ${sample_description_col}
+        --ncomp ${ncomp}
+        ${correlation}
+        --scheme ${adv.scheme}
+        --mode ${adv.mode}
+        --maxiter ${adv.maxiter}
+        ${adv.scale}
+        --init ${adv.init}
+        --tol ${adv.tol}
+        ${adv.nearzerovar}
+        --rdata_out ${rdata_out}
+        --sample_metadata_out ${sample_metadata_out}
+        --variable_metadata_outdir outdir
+        ]]>
+    </command>
+
+    <inputs>
+        <repeat name="blocks" title="Blocks">
+            <param name="block_name" type="text" label="Block name" />
+            <param name="keep" type="integer" value="0" min="0" label="Number of variables to select for each component" help="Default is to keep all variables" />
+            <param name="data_matrix" type="data" format="tabular" label="Data matrix" help="rows = variables, columns = samples" />
+            <param name="variable_metadata" type="data" format="tabular" optional="true" label="Variables metadata" help="rows = variables" />
+        </repeat>
+        <param name="sample_metadata_in" type="data" format="tabular" label="Samples metadata matrix" />
+        <param name="sample_description_col" type="integer" value="0" min="0" label="Sample description column number" help="Use the last column by default" />
+        <param name="ncomp" type="integer" value="2" min="1" label="Number of components to include in the model" />
+        <param name="correlation" type="boolean" truevalue="--correlation" falsevalue="" checked="false" label="Correlation between all blocks"/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="scheme" type="select" label="Scheme">
+                <option value="horst" selected="true">horst</option>
+                <option value="factorial"            >factorial</option>
+                <option value="centroid"             >centroid</option>
+            </param>
+            <param name="mode" type="select" label="Mode">
+                <option value="regression" selected="true">regression</option>
+                <option value="canonical"                 >canonical</option>
+                <option value="invariant"                 >invariant</option>
+                <option value="classic"                   >classic</option>
+            </param>
+            <param name="maxiter" type="integer" value="100" min="1" label="Maximum number of iterations" />
+            <param name="scale" type="boolean" truevalue="--scale" falsevalue="" checked="true" label="Scale" help="if checked, each block is standardized to zero means and unit variances" />
+            <param name="init" type="select" label="Init">
+                <option value="svd" selected="true">svd</option>
+                <option value="svd.single"         >svd.single</option>
+            </param>
+            <param name="tol" type="float" value="1e-06" min="0" label="Convergence stopping value (tol)" />
+            <param name="nearzerovar" type="boolean" truevalue="--nearzerovar" falsevalue="" checked="false" label="Should be set to TRUE in particular for data with many zero values" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="rdata_out" format="rdata" label="${tool.id}_output.rdata" />
+        <data name="sample_metadata_out" format="tabular" label="${tool.id}_${sample_metadata_in.name}" />
+        <collection name="blocks_output" type="list" label="${tool.id}_blocks_output">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="outdir" format="tabular" />
+        </collection>
+    </outputs>
+
+    <tests>
+        <test>
+            <repeat name="blocks">
+                <param name="block_name" value="Block1" />
+                <param name="data_matrix" value="in_block1_data.tabular" />
+            </repeat>
+            <repeat name="blocks">
+                <param name="block_name" value="Block2" />
+                <param name="data_matrix" value="in_block2_data.tabular" />
+            </repeat>
+            <param name="sample_metadata_in" value="in_sample_meta.tabular" />
+            <output name="rdata_out" value="out_rdata.rdata" />
+            <output name="sample_metadata_out" value="out_sample_meta.tabular" />
+        </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 blocks.splsda
+======================
+
+-----------
+Description
+-----------
+
+The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets.
+Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis.
+
+-----------
+Input files
+-----------
+
+For each block (min 2 blocks):
+==============================
+
++------------------------------+------------+
+| Parameter : num + label      |   Format   |
++==============================+============+
+| 1 : Data matrix              |   tabular  |
++------------------------------+------------+
+| 2 : [opt] Variables metadata |   tabular  |
++------------------------------+------------+
+
+Variables metadata files are optional.
+If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
+
+Global input files:
+===================
+
++-----------------------------+------------+
+| Parameter : num + label     |   Format   |
++=============================+============+
+| 1 : Samples metadata        |   tabular  |
++-----------------------------+------------+
+
+By default, the last column of the samples metadata matrix will be used as samples description factors.
+If it's not the case, the column number can be inputed in the `Sample description column number` parameter.
+
+----------
+Parameters
+----------
+
+For each block (min 2 blocks):
+==============================
+
+Block name
+    Name of the block. If not provided, this will default to the input filename
+
+Number of variables to select for each component
+    If set to 0 (default), all variables will be considered in the model
+
+Global parameters:
+==================
+
+Sample description column number
+
+Number of components to include in the model
+
+Correlation between all blocks
+
+Advanced options:
+=================
+
+Scheme
+
+Mode
+
+Maximum number of iterations
+
+Scale
+
+Init
+
+Convergence stopping value (tol)
+
+Near zero var
+
+------------
+Output files
+------------
+
+mixomics_blocksplsda_output.rdata
+    | rData output
+    | Contains the `mixomics_result` R object containing the result of the block.splsda function
+
+mixomics_blocksplsda_{input_sample_metadata_name}
+    | tabular output
+    | Identical to the input Sample metadata file with appended columns from the result of block.splsda function
+
+mixomics_blocksplsda_blocks_output
+    A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block
+
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
+    </citations>
+
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_blocksplsda_script.R	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,213 @@
+#!/usr/bin/env Rscript
+
+# Setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+## Get parameters ##
+suppressPackageStartupMessages(require(argparse))
+
+parser <- ArgumentParser(description='Run the mixOmics block.splsda function')
+
+parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, help="Block name + nb variables to select + data matrix file + variables metadata file")
+parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, help="Samples metadata file")
+parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number")
+parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, help="Number of components to include in the model")
+parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks")
+parser$add_argument('--scheme', dest='scheme', required=TRUE, help="Scheme")
+parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode")
+parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, help="Maximum number of iterations")
+parser$add_argument('--scale', dest='scale', action="store_true", help="Each block is standardized to zero means and unit variances")
+parser$add_argument('--init', dest='init', required=TRUE, help="Init (svd or svd.single)")
+parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value")
+parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", help="Should be set in particular for data with many zero values")
+parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
+parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
+parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
+
+args <- parser$parse_args()
+
+## Print parameters
+print("Blocks:")
+print(args$blocks_list)
+print("Sample metadata file:")
+print(args$sample_metadata_in)
+print("Sample description column number:")
+print(args$sample_description_col)
+print("Number of components:")
+print(args$ncomp)
+print("Compute correlation between all blocks:")
+print(args$correlation)
+print("Scheme:")
+print(args$scheme)
+print("Mode:")
+print(args$mode)
+print("Max nb of iterations:")
+print(args$maxiter)
+print("Scale:")
+print(args$scale)
+print("Tol:")
+print(args$tol)
+print("near.zero.var:")
+print(args$nearzerovar)
+print("Output Rdata file:")
+print(args$rdata_out)
+print("Output sample metadata file:")
+print(args$sample_metadata_out)
+print("Output variable metadata directory:")
+print(args$variable_metadata_outdir)
+
+## Loading libraries
+suppressPackageStartupMessages(require(mixOmics))
+
+## Read sample metadata file and set description factor matrix
+sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1)
+sample_metadata_names <- row.names(sample_metadata)
+# print(sample_metadata_names)
+
+# print("Sample metadata matrix:")
+# print(head(sample_metadata))
+
+description_column <- ncol(sample_metadata)
+if(args$sample_description_col > 0)
+{
+    description_column <- args$sample_description_col
+}
+
+Y <- factor(sample_metadata[[description_column]])
+
+print("Y factor matrix:")
+print(Y)
+
+## Read and prepare block datasets
+list_X <- c()
+keepX <- c()
+
+for(i in 1:nrow(args$blocks_list))
+{
+    # Read block input parameters
+    block_name <- args$blocks_list[i,1]
+    block_keep <- strtoi(args$blocks_list[i,2])
+    block_data_matrix_filename <- args$blocks_list[i,3]
+    # block_meta_var <- args$blocks_list[i,4]
+
+    print(sprintf("Processing block %s", block_name))
+
+    # Store block data matrices
+    block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns
+    block_data_matrix_names <- row.names(block_data_matrix)
+    # print(block_data_matrix_names)
+
+    if(!identical(sample_metadata_names, block_data_matrix_names))
+    {
+        stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix")
+    }
+
+    list_X[[block_name]] <- block_data_matrix
+
+    # Set the nb of variables to keep
+    nb_variables = ncol(list_X[[block_name]])
+    if(block_keep > 0)
+    {
+        keepX[[block_name]] <- rep(block_keep, args$ncomp)
+    }
+    else
+    {
+        keepX[[block_name]] <- rep(nb_variables, args$ncomp)
+    }
+    print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep))
+}
+
+# print(list_X)
+
+## Generate design matrix
+block_nb <- nrow(args$blocks_list)
+
+design <- matrix(0, nrow = block_nb, ncol = block_nb)
+
+if(args$correlation)
+{
+    design <- matrix(1, nrow = block_nb, ncol = block_nb)
+    diag(design) <- 0
+}
+
+# print("Design matrix:")
+# print(design)
+
+###################
+## Main function ##
+###################
+
+mixomics_result <- block.splsda(X = list_X,
+                                 Y = Y,
+                                 ncomp = args$ncomp,
+                                 keepX = keepX,
+                                 design = design,
+                                 scheme = args$scheme,
+                                 mode = args$mode,
+                                 scale = args$scale,
+                                 init = args$init,
+                                 tol = args$tol,
+                                 max.iter = args$maxiter,
+                                 near.zero.var = args$nearzerovar,
+                                 all.outputs = TRUE)
+
+print("Block.splsda object:")
+print(mixomics_result)
+
+## Save output Rdata file
+save(mixomics_result, file=args$rdata_out)
+
+## Save output sample metadata file
+# print("Block.splsda variates:")
+# print(mixomics_result$variates)
+
+for(bname in names(mixomics_result$variates))
+{
+    # print(bname)
+    # print(mixomics_result$variates[[bname]])
+
+    # Format the column names to add the block name and replace spaces
+    colnames(mixomics_result$variates[[bname]]) <- paste("block.splsda", bname, gsub(" ", "_", colnames(mixomics_result$variates[[bname]])), sep = "_")
+    # print(mixomics_result$variates[[bname]])
+
+    # Append the new columns to the sample metadata matrix
+    sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[bname]])
+}
+
+# print(sample_metadata)
+
+write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
+
+## Save output variable metadata files in output directory
+# print("Block.splsda loadings:")
+# print(mixomics_result$loadings)
+
+for(i in 1:nrow(args$blocks_list))
+{
+    # Read again block input parameters
+    block_name <- args$blocks_list[i,1]
+    # block_keep <- strtoi(args$blocks_list[i,2])
+    # block_data_matrix_filename <- args$blocks_list[i,3]
+    block_meta_var <- args$blocks_list[i,4]
+
+    meta_variable <- mixomics_result$loadings[[block_name]]
+    # print(head(meta_variable))
+
+    # Read input block variable metadata files if provided (optional)
+    if(block_meta_var != "None")
+    {
+        input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)
+        # print(head(input_meta_variable))
+
+        # Append the new columns to the variable metadata matrix
+        meta_variable <- cbind2(input_meta_variable, meta_variable)
+    }
+
+    # print(head(meta_variable))
+
+    block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="")
+    write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
+}
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotindiv.xml	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,107 @@
+<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="0.1.0" 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)"/>
+        <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 (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 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>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotindiv_script.R	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env Rscript
+
+# Setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+## Main Function ##
+
+suppressPackageStartupMessages(require(argparse))
+
+parser <- ArgumentParser(description='Run the mixOmics plotIndiv function')
+
+parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
+parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend")
+parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots")
+parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
+
+args <- parser$parse_args()
+
+##
+print("Input RData:")
+print(args$input_rdata)
+print("Plot legend:")
+print(args$legend)
+print("Plot ellipse plots:")
+print(args$ellipse)
+print("Output PDF file:")
+print(args$output_pdf)
+
+# loading libraries
+suppressPackageStartupMessages(require(mixOmics))
+
+load(args$input_rdata)
+
+pdf(args$output_pdf)
+
+plotIndiv(mixomics_result,
+          legend = args$legend,
+          ellipse = args$ellipse)
+
+for(k in 1:(length(mixomics_result$names[[3]])-1))
+{
+    name_block = mixomics_result$names[[3]][k]
+
+    plotIndiv(mixomics_result,
+              blocks = k,
+              legend = args$legend,
+              ellipse = args$ellipse)
+}
+
+dev.off()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotvar.xml	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,107 @@
+<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="0.85" 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>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotvar_script.R	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env Rscript
+
+# Setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+## Main Function ##
+
+suppressPackageStartupMessages(require(argparse))
+
+parser <- ArgumentParser(description='Run the mixOmics plotVar function')
+
+parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
+parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend")
+parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)")
+parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
+
+args <- parser$parse_args()
+
+##
+print("Input RData:")
+print(args$input_rdata)
+print("Plot legend:")
+print(args$legend)
+print("Cutoff:")
+print(args$cutoff)
+print("Output PDF file:")
+print(args$output_pdf)
+
+# loading libraries
+suppressPackageStartupMessages(require(mixOmics))
+
+load(args$input_rdata)
+
+pdf(args$output_pdf)
+
+plotVar(mixomics_result,
+        legend = args$legend,
+        cutoff = args$cutoff)
+
+for(k in 1:(length(mixomics_result$names[[3]])-1))
+{
+    name_block = mixomics_result$names[[3]][k]
+
+    plotVar(mixomics_result,
+            blocks = k,
+            legend = args$legend,
+            cutoff = args$cutoff)
+}
+
+dev.off()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in_block1_data.tabular	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,7 @@
+	"A1"	"A2"	"B1"	"B2"
+"var1"	1	2	3	4
+"var2"	1.5	2.5	3.5	4.5
+"var3"	2.5	2	2.5	2
+"var4"	5	4	3	2
+"var5"	1.001	1.01	1.1	1
+"var6"	10	13	11	10

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in_block2_data.tabular	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,7 @@
+	"A1"	"A2"	"B1"	"B2"
+"var1"	2	3	4	5
+"var2"	2.5	1	2.5	4
+"var3"	2.5	2	2.5	2
+"var4"	6	5	3	2
+"var5"	10.001	10.01	10.1	10
+"var6"	20	23	21	20

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in_sample_meta.tabular	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,5 @@
+	"Y"
+"A1"	"catA"
+"A2"	"catA"
+"B1"	"catB"
+"B2"	"catB"

Binary file test-data/out_plotIndiv.pdf has changed

Binary file test-data/out_plotVar.pdf has changed

Binary file test-data/out_rdata.rdata has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_sample_meta.tabular	Fri May 17 05:00:22 2019 -0400
@@ -0,0 +1,5 @@
+""	"Y"	"block.splsda_Block1_comp1"	"block.splsda_Block1_comp2"	"block.splsda_Block2_comp1"	"block.splsda_Block2_comp2"	"block.splsda_Y_comp1"	"block.splsda_Y_comp2"
+"A1"	"catA"	1.85013467343542	0.422684485040581	1.28016568038406	0.405956759170116	1.22474487139159	0.0342790721507239
+"A2"	"catA"	1.07324868851916	-0.960001503242697	1.53872954309497	-0.749531756995324	1.22474487139159	-0.16259622770647
+"B1"	"catB"	-1.0856729590951	1.64317643604658	-1.01949098398762	1.60513370686125	-1.22474487139159	0.374128476201717
+"B2"	"catB"	-1.83771040285949	-1.10585941784446	-1.79940423949142	-1.26155870903602	-1.22474487139159	-0.245811320645977