<tool id="secimtools_modify_design_file" name="Modify design file" version="@WRAPPER_VERSION@">
    <description>to remove specified group types or sampleIDs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
modify_design_file.py
--input $input
--design $design
--uniqID $uniqID
#if $group
    --group $group
#end if
--drops $toDrop
--out $out
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
        <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
        <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s) or Sample(s), comma separated, to remove from your design file."/>
    </inputs>
    <outputs>
        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
    </outputs>
    <tests>
        <test>
            <param name="input"  value="ST000006_data.tsv"/>
            <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
            <param name="uniqID" value="Retention_Index" />
            <param name="group"  value="White_wine_type_and_source_no_space" />
            <param name="toDrop" value="Chardonnay_Napa_CA2003,Riesling_CA2004,SauvignonBlanc_LakeCounty_CA2001" />
            <output name="out"   file="ST000006_modify_design_output.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool creates a new design file based on the existing wide dataset and design file where the specified group types or samples are removed from the existing design file.

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

**Input**

    - Two input datasets are required.

@WIDE@

**NOTE:** The sample IDs must match the sample IDs in the Design File
(below). Extra columns will automatically be ignored.

@METADATA@

@UNIQID@

**Group/Treatment [Optional]**

    - Name of the column in your Design File that contains group classifications. If not provided, the drop will be performed by 'sampleID's.

**Group(s)/Sample(s) to drop**

    - Name of the Group(s) or Sample(s), comma separated, to remove from the design file.

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

**Output**

This tool will output a single design file that contains only the samples not selected for removal.

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