<tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">

    <description>determine the correlation circles that can be overlaid and compute the correlations</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_matcoraddvar.R

        --input_rdata ${input_rdata}
        --block_Y_file ${block_Y}

        ##--cutoff_comp ${cutoff_comp}
        --cutoff_comp 0.75
        #if str($var_of_interest_file) !='':
            --interest_var_file ${var_of_interest_file}
        #end if

        --output_rdata ${output_rdata}
        --output_response_var ${output_response_var}
        --output_blocks_comb ${output_blocks_comb}

        @COMMAND_LOG_EXIT@

    ]]></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="block_Y" type="data" format="tabular"
               label="Block Y"
               help="[block_Y] (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 Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
        <!-- 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="variables not belonging to any block will not be considered"/>
        <!-- <param name="cutoff_comp" type="float" value="0.775" 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." /> -->
    </inputs>

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

    <tests>
    </tests>

    <help><![CDATA[

@HELP_AUTHORS@

======================
visCorVar matCorAddVar
======================

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

Bla bla...

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

**Upstream tools**

======================= =================================== ========
Name                    Output file                         Format
======================= =================================== ========
mixOmics.block.splsda   mixomics_blocksplsda_output.RData   rdata
======================= =================================== ========

**Downstream tools**

================================ ========================================= ========
Name                             Output file                               Format
================================ ========================================= ========
visCorVar.circleCor              viscorvar_matcoraddvar_output.RData       rdata
-------------------------------- ----------------------------------------- --------
visCorVar.computeMatSimilarity   viscorvar_matcoraddvar_output.RData       rdata
-------------------------------- ----------------------------------------- --------
visCorVar.networkVar             viscorvar_matcoraddvar_response_var.tsv   tabular
================================ ========================================= ========

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

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

+---------------------------------+------------+
| Parameter : num + label         |   Format   |
+=================================+============+
| 1 : Rdata block.splsda output   |   Rdata    |
+---------------------------------+------------+
| 2 : Block Y                     |   tabular  |
+---------------------------------+------------+
| 3 : [opt] Variables of interest |   txt      |
+---------------------------------+------------+

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

@HELP_MANUAL@

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

viscorvar_matcoraddvar_output.RData
    RData output

viscorvar_matcoraddvar_response_var.tsv


viscorvar_matcoraddvar_blocks_comb.tsv


    ]]></help>

    <expand macro="citations" />

</tool>