<tool id="viscorvar_circlecor" name="visCorVar circleCor" version="@TOOL_VERSION@+galaxy1" 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>

    <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_circlecor.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_LOG_EXIT@

    ]]></command>

    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file"
               help="output RData from matCorAddVar"/>
        <param name="blocks_vec_list" type="data" format="tabular"
               label="List of blocks vector."
               help="output *_blocks_comb.tsv file from matCorAddVar"/>
        <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="tabular"
               label="List of response variables"
               help="output *_response_var.tsv file from matCorAddVar"/>
        <param name="select_responses_var" type="select" display="checkboxes"
               multiple="true" label="Response variables"
               help="select the response variables which will be plotted in the correlation circle">
        <!-- <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="${tool.name}_selected_var.tsv" />
        <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
    </outputs>

    <tests>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

===================
visCorVar circleCor
===================

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

Bla bla...

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

**Upstream tools**

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

**Downstream tools**

====================== ====================================== =========
Name                   Output file                            Format
====================== ====================================== =========
visCorVar.networkVar   viscorvar_circlecor_selected_var.tsv   tabular
====================== ====================================== =========

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

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

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

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

@HELP_MANUAL@

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

viscorvar_circlecor.pdf
    Correlation circle pdf file

viscorvar_circlecor_selected_var.tsv
	List of variables selected in the correlation circle

    ]]></help>

    <expand macro="citations" />

</tool>