<tool id="viscorvar_computematsimilarity" name="visCorVar computeMatSimilarity" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">

    <description>performs the computation of the similarities. The similarity between two variables is an approximation of the correlation between these two variables.</description>

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

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command detect_errors="aggressive"><![CDATA[

        @COMMAND_RSCRIPT@/viscorvar_computematsimilarity.R

        --input_rdata ${input_rdata}

        --output_rdata ${output_rdata}

    ]]></command>
    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file"
               help="this is the RData output file from matCorAddVar function"/>
    </inputs>

    <outputs>
        <data name="output_rdata" format="rdata" label="${tool.name}_output.RData" />
    </outputs>

    <tests>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

==============================
visCorVar computeMatSimilarity
==============================

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

This tool is a pre-processing step in order to create networks. It computes an
approximation of the correlation between a variable of a omics dataset and a variable of
an other omics dataset.

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

**Upstream tools**

======================== ===================================== ========
Name                     Output file                           Format
======================== ===================================== ========
visCorVar.matCorAddVar   viscorvar_matcoraddvar_output.RData   rdata
======================== ===================================== ========

**Downstream tools**

====================== ============================================= ========
Name                   Output file                                   Format
====================== ============================================= ========
visCorVar.networkVar   viscorvar_computematsimilarity_output.RData   rdata
====================== ============================================= ========

---------------------------------------------------

-----------
Input files
-----------

+------------------------------------------+------------+
| Parameter : num + label                  |   Format   |
+==========================================+============+
| 1 : Rdata visCorVar.matCorAddVar output  |   Rdata    |
+------------------------------------------+------------+

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

@HELP_MANUAL@

------------
Output files
------------

viscorvar_computematsimilarity_output.RData
    | RData output
    | Contains the `computeMatSimilarity_result` R object containing the result of the computeMatSimilarity function


    ]]></help>

    <expand macro="citations" />

</tool>