annotate viscorvar_circlecor.xml @ 4:d4e9f7546dfa draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"

<tool id="viscorvar_circlecor" name="visCorVar circleCor" version="@TOOL_VERSION@+galaxy0" 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="this is the RData output file from the matCorAddVar function"/>
        <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="each element of List of blocks vector contain blocks for which selected variables can
               be visualized in the correlation circle">
            <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="choose 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
-----------

This tool allows visualizing variables of omics datasets which are correlated with
the response variables thanks to correlation circles. The determination of the omics
datasets which can be visualized is made by the tool matCorAddVar. This tool performs
a zoom in a rectangle to retrieve omics datasets variables which are correlated with a
response variable. 

-----------------
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>