<tool id="networkVar" name="networkVar" version="0.4.0" 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>

    <requirements>
        <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
        <requirement type="package" version="1.2">r-igraph</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__}/networkVar_wrapper.R
        --mat_similarity_rdata ${mat_similarity_rdata}
        --block_splsda_rdata ${block_splsda_rdata}
        --var_list_file ${var_list_file}

        #if str($var_of_interest_file) !='':
            --interest_var_file ${var_of_interest_file}
        #end if

        --responses_var ${select_responses_var}

        --output_graph ${output_graph}
        ]]>
    </command>

    <inputs>
        <param name="mat_similarity_rdata" type="data" format="rdata"
               label="Input computeMatSimilarity RData file"
               help="output RData file from computeMatSimilarity"/>
        <param name="block_splsda_rdata" type="data" format="rdata"
               label="Input block.SPLSDA RData file"
               help="output Rdata file from block.SPLSDA"/>
        <param name="var_list_file" type="data" format="tabular"
               label="Variables list file"
               help="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="responses_var_list" type="data" format="txt"
               label="List of response variables"
               help="list of the response variables that will be in the network"/>
        <param name="select_responses_var" type="select" display="checkboxes" multiple="true"
               label="Response variables">
        <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
            <options from_dataset="responses_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>
    </help>

</tool>