<tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">

    <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link 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_networkvar.R

        --mat_similarity_rdata ${mat_similarity_rdata}
        --var_list_file ${var_list_file}
        --response_var ${select_response_var}

        --output_graph ${output_graph}

        @COMMAND_LOG_EXIT@

    ]]></command>

    <inputs>
        <param name="mat_similarity_rdata" type="data" format="rdata"
               label="Input computeMatSimilarity RData file"
               help="output RData file from computeMatSimilarity"/>
        <param name="var_list_file" type="data" format="tabular"
               label="Variables list file"
               help="selected variables output tabular file from circleCor"/>

        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
        <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
               label="Variables of interest (Optional)"
               help="these variables have to belong to datasets that can be superimposed"/> -->

        <param name="response_var_list" type="data" format="tabular"
               label="List of response variables"
               help="output *_response_var.tsv file from matCorAddVar"/>
        <param name="select_response_var" type="select" display="checkboxes" multiple="true"
               label="Response variables"
               help="response variables that will be plotted in the network">
        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
            <options from_dataset="response_var_list">
                <column name="value" index="0"/>
                <filter type="unique_value" column="0"/>
                <filter type="sort_by" name="sorted_value" column="0"/>
            </options>
        </param>
    </inputs>

    <outputs>
        <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
    </outputs>

    <tests>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

====================
visCorVar networkVar
====================

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

Bla bla...

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

**Upstream tools**

================================ ============================================= =========
Name                             Output file                                   Format
================================ ============================================= =========
visCorVar.computeMatSimilarity   viscorvar_computematsimilarity_output.RData   rdata
-------------------------------- --------------------------------------------- ---------
visCorVar.circleCor              viscorvar_circlecor_selected_var.tsv          tabular
-------------------------------- --------------------------------------------- ---------
visCorVar.matCorAddVar           viscorvar_matcoraddvar_response_var.tsv       tabular
================================ ============================================= =========

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

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

+-------------------------------------------------------+------------+
| Parameter : num + label                               |   Format   |
+=======================================================+============+
| 1 : Rdata visCorVar.computeMatSimilarity output       |   rdata    |
+-------------------------------------------------------+------------+
| 2 : *_selected_var.tsv visCorVar.circleCor output     |   tabular  |
+-------------------------------------------------------+------------+
| 3 : *_response_var.tsv visCorVar.matCorAddVar output  |   tabular  |
+-------------------------------------------------------+------------+

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

@HELP_MANUAL@

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

viscorvar_networkvar_graph.graphml
	GraphML file

    ]]></help>

    <expand macro="citations" />

</tool>