comparison mixomics_blocksplsda.xml @ 4:d4e9f7546dfa draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"

3:df8428358b7f

<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy1" 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>

    <macros>
        <import>macros.xml</import>

        --rdata_out ${rdata_out}
        ##--sample_metadata_out ${sample_metadata_out}
        --variable_metadata_outdir outdir

        @COMMAND_LOG_EXIT@

    ]]></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="[keep] Estimation of the number of variables in the block correlated with variables from the other blocks and correlated with response variables. If set to 0, all variables will be selected." />
            <param name="data_matrix" type="data" format="tabular"
                   label="Data matrix"
                   help="Block data in tabular format (rows = variables, columns = samples). The first column contains the variables names and the first row contains the samples names. Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values." />
            <param name="variable_metadata" type="data" format="tabular" optional="true"
                   label="Variables metadata [optional]"
                   help="Variables metadata in tabular format (rows = variables). The first colum contains the variables names. The first row contains the metadata column names. The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created." />
        </repeat>
        <param name="sample_metadata_in" type="data" format="tabular"
               label="Samples metadata"
               help="Samples metadata in tabular format (rows = samples). The first column contains the sample names. The first row contains the metadata column names. Samples names must be in the same order (transposed) than all the blocks. One of the column (the last by default) must contain the samples groups for integration." />
        <param name="sample_description_col" type="integer" value="0" min="0"
               label="Samples groups column number"
               help="Column from the samples metadata file containing samples groups. If set to 0, the last column will be used." />
        <param name="correlation" type="boolean" truevalue="--correlation"
               falsevalue="" checked="false"
               label="Correlation between all blocks"
               help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="ncomp" type="integer" value="2" min="1"
                   label="Number of components to include in the model"
                   help="[ncomp] Number of new variables (components) computed by the data integration." />
            <!-- <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>

                <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"
                   help="[max.iter] Maximum number of iterations performed by block.splsda." />
            <!-- <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="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true"
                   label="Check for missing values"

            <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[

-----------
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.

-----------------
Workflow position
-----------------

| 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
----------

4:d4e9f7546dfa

<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" 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>

    <macros>
        <import>macros.xml</import>

        --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="estimation of the number of variables of the block correlated with variables of the other blocks and correlated with response variables. If set to 0, all variables will be selected" />
            <param name="data_matrix" type="data" format="tabular"
                   label="Data matrix"
                   help="data matrix contains the values of the variables. For the file structure, see below in the section Input files" />
            <param name="variable_metadata" type="data" format="tabular" optional="true"
                   label="Variables metadata [optional]"
                   help="variables metadata contains the metadata of the variables. For the file structure, see below in the section Input files" />
        </repeat>
        <param name="sample_metadata_in" type="data" format="tabular"
               label="Samples metadata"
               help="samples metadata contains the metadata of the samples. For the file structure, see below in the section Global input files" />
        <param name="sample_description_col" type="integer" value="0" min="0"
               label="Samples groups column number"
               help="column from the samples metadata file containing samples groups. If set to 0, the last column will be used" />
        <param name="correlation" type="boolean" truevalue="--correlation"
               falsevalue="" checked="false"
               label="Correlation between all blocks"
               help="if set to Yes, data integration will take into account correlations between all the blocks. If set to No, data integration will only take into account correlations between the blocks and the response" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="ncomp" type="integer" value="2" min="1"
                   label="Number of components to include in the model"
                   help="number of new variables (components) computed by the data integration" />
            <!-- <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>

                <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"
                   help="maximum number of iterations performed by block.splsda" />
            <!-- <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="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true"
                   label="Check for missing values"

            <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" />
            <!-- <param name="correlation" value=true /> -->
            <output name="rdata_out" value="mixomics_blocksplsda_output.rdata" />
            <!-- <output name="sample_metadata_out" value="out_sample_meta.tabular" /> -->
        </test>
    </tests>

    <help><![CDATA[

-----------
Description
-----------

The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets.
This data integration takes as input parameters different omics datasets
(transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response
variable is equal to « Treated »  or « Control »). This data integration returns, for each omics dataset, variables
which are correlated with the variables of the other omic datasets and the response variable. The other functions of
this pipeline allow visualizing this correlated variables thanks to correlation circles and networks.

-----------------
Workflow position
-----------------

| 1 : Data matrix              |   tabular  |
+------------------------------+------------+
| 2 : [opt] Variables metadata |   tabular  |
+------------------------------+------------+

1. Data matrix structure
The data matrix is in tabular format (.tsv).
The first column contains the variables names.
The first row contains the samples names.
Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values.

2. Variables metadata structure
The variables metadata is in tabular format (.tsv).
The first colum contains the variables names.
The first row contains the metadata column names.
The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created.

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  |
+-----------------------------+------------+

1. Samples metadata structure
Samples metadata is in tabular format (.tsv).
The first column contains the sample names.
The first row contains the metadata column names.
Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for integration.

----------
Parameters
----------