circleCor.xml

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

    <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response variables.</description>

    <requirements>
        <requirement type="package">r-base</requirement>
        <requirement type="package" version="0.4">r-ellipse</requirement>
        <requirement type="package" version="2.0">r-argparse</requirement>
        <requirement type="package" version="1.1">r-rcolorbrewer</requirement>

        <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
    </requirements>

    <stdio>
        <!-- <exit_code range="1:" level="fatal" /> -->
    </stdio>

    <command detect_errors="aggressive">
        <![CDATA[
        Rscript
        ${__tool_directory__}/circleCor_wrapper.R
        --input_rdata ${input_rdata}
        --blocks_vec ${select_blocks.value}
        --responses_var ${select_responses_var}
        --x_min ${x_min}
        --x_max ${x_max}
        --y_min ${y_min}
        --y_max ${y_max}
        --output_var ${output_var}
        --output_pdf ${output_pdf}
        ]]>
    </command>

    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file"
               help="output RData from matCor_addVar"/>
        <param name="blocks_vec_list" type="data" format="tabular"
               label="List of blocks vector."
               help="output tsv file from matCor_addVar"/>
        <param name="select_blocks" type="select"
               label="Blocks"
               help="list of the blocks that are to be superimposed">
            <options from_dataset="blocks_vec_list">
                <column name="value" index="0"/>
                <filter type="unique_value" column="0"/>
                <filter type="sort_by" name="sorted_value" column="0"/>
            </options>
        </param>
        <param name="responses_var_list" type="data" format="txt"
               label="List of response variables"
               help="list of the response variables which will be plotted in the correlation circle"/>
        <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>
        <param name="x_min" type="float" value="-1" min="-1" max="1"
               label="X min" help="" />
        <param name="x_max" type="float" value="1" min="-1" max="1"
               label="X max" help="" />
        <param name="y_min" type="float" value="-1" min="-1" max="1"
               label="Y min" help="" />
        <param name="y_max" type="float" value="1" min="-1" max="1"
               label="Y max" help="" />
    </inputs>

    <outputs>
        <data name="output_var" format="tabular" label="${tool.name}_var.tsv" />
        <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
    </outputs>

    <tests>
    </tests>

    <help>
    </help>

</tool>