comparison viscorvar_circlecor.xml @ 5:88c1fd2ac110 draft default tip

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"

4:d4e9f7546dfa

        --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">

                <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">

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

+-----------------------------------------------------------+-----------+
| 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
----------

viscorvar_circlecor.pdf
    Correlation circle pdf file

viscorvar_circlecor_selected_var.tsv
	List of variables selected in the correlation circle

    ]]></help>

    <expand macro="citations" />

5:88c1fd2ac110

        --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="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 the matCorAddVar function."/>
        <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">

                <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 the matCorAddVar function"/>
        <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">

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

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

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

+-----------------------------------------------------------+-----------+
| 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
----------

viscorvar_circlecor.pdf
    Correlation circle pdf file

viscorvar_circlecor_selected_var.tsv
	List of selected variables which are contained in a rectangle of the correlation circle

    ]]></help>

    <expand macro="citations" />