<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="0.2.0" 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="${tool.name}_output.rdata" />
        <data name="sample_metadata_out" format="tabular" label="${tool.name}_${sample_metadata_in.name}" />
        <collection name="blocks_output" type="list" label="${tool.name}_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.

1. Data matrix format
    * Rows = variables, Columns = samples
    * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed)
    * First column = variables name

2. Variables metadata format
    * Rows = variables, Columns = metadata
    * First row = metadata column names
    * First column = variables names. MUST be the same and in the same order than in the associated data matrix

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.

1. Samples metadata format
    * Rows = samples, Columns = metadata
    * First row = metadata column names
    * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices

----------
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>