<tool id="secimtools_generate_rank_wide" name="Ranked wide file"  version="@WRAPPER_VERSION@">
    <description>Generate a wide format file with ranked columns from an input wide file.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
addGroupRank.py
--wide $wide
--design $design
--out $out
#if $ngroup:
    --ngroup $ngroup
#end if
--rank $rank
--uniqID $uniqID
    ]]></command>
    <inputs>
        <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
        <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/>
        <param name="rank" type="text" size="30" value="Rank" label=" Name of flag column" help="The column name in your design file that contains the flags to specify whether a sampleID will be ranked in the input wide file."/>
    </inputs>
    <outputs>
        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/>
    </outputs>

    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool is used to generate a wide format file with each column being ranked in the input wide format dataset.

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**Input**

    - Two input datasets are required.


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**Output**

The user will get a output file from the tool:

(1) a wide format file with each column being ranked. The columns will be selected using the flag column in the design file.


    ]]></help>
    <expand macro="citations"/>
</tool>