<tool id="normalize_dataset" name="Normalize a dataset by" version="0.1.0">
    <description>row or column sum to obtain proportion or percentage</description>

    <requirements>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>

    <version_command></version_command>

    <command><![CDATA[
        python $__tool_directory__/normalize_dataset.py
            --input_file $input_file
            --output_file $output_file
            --normalization $normalization
            --format $format
    ]]></command>

    <inputs>
        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>

        <param name="normalization" label="Normalization on" type="select" help="(--normalization)">
            <option value="column" selected="True">Column</option>
            <option value="row">Row</option>
        </param>

        <param name="format" label="Output format" type="select" help="(--format)">
            <option value="proportion" selected="True">Proportion</option>
            <option value="percentage">Percentage</option>
        </param>
    </inputs>

    <outputs>
        <data name="output_file" format="tabular"
            label="${tool.name} on ${on_string}: Normalized dataset" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="input_file.tabular"/>
            <param name="normalization" value="column"/>
            <param name="format" value="proportion"/>
            <output name="output_file" file="output_column_proportion.tabular"/>
        </test>
        <test>
            <param name="input_file" value="input_file.tabular"/>
            <param name="normalization" value="row"/>
            <param name="format" value="proportion"/>
            <output name="output_file" file="output_row_proportion.tabular"/>
        </test>
        <test>
            <param name="input_file" value="input_file.tabular"/>
            <param name="normalization" value="column"/>
            <param name="format" value="percentage"/>
            <output name="output_file" file="output_column_percentage.tabular"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

This tool normalizes each row or column of a dataset by the row or column sum.
The results can be in proportion or percentage.

The input file must be in tabular format with tab-separated columns. Only data will be used for normalization.
    ]]></help>

    <citations>
    </citations>
</tool>