<tool id="matCor_addVar" name="matCor_addVar" version="0.3.0" profile="16.04" workflow_compatible="true">

    <description>computes all the correlations needed to plot a correlation circle and determines which correlation circles can be superimposed</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[
        Rscript
        ${__tool_directory__}/matCor_addVar_wrapper.R
        --input_rdata ${input_rdata}
        --cutoff_comp ${cutoff_comp}
        --mat_block_Y_file ${mat_block_Y}
        --output_rdata ${output_rdata}
        --output_blocks_comb ${output_blocks_comb}
        ]]>
    </command>

    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file from block.SPLSDA"
               help="This is the RData output file from the block.splsda function." />
        <param name="cutoff_comp" type="float" value="0.8" min="0" max="1"
               label="Cutoff comp"
               help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." />
        <param name="mat_block_Y" type="data" format="tabular"
               label="Matrix Block Y"
               help="Matrix Block Y in tabular format. This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Matrix Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
    </inputs>

    <outputs>
        <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
        <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
    </outputs>

    <tests>
    </tests>

    <help>
    </help>

</tool>