<tool id="table_pandas_transform" name="table column transformations" version="@PANDAS_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>apply transformations on multiple columns</description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <expand macro="requirement_pandas_pyarrow"/>
    </requirements>
    <required_files>
        <include path="table_pandas_transform.py" />
        <include path="utils.py" />
    </required_files>
    <expand macro="creator" />
    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/table_pandas_transform.py' 
            --input_dataset '$input_dataset' '$input_dataset.ext' 
            --columns '$columns' 
            --transformation '$transformation' 
            --output_dataset '$output_dataset' '$output_dataset.ext'
    ]]></command>
    <inputs>
        <param name="input_dataset" type="data" format="csv,tsv,tabular,parquet" label="Input Dataset"/>
        <param name="columns" type="data_column" data_ref="input_dataset" use_header_names="true" multiple="true" label="Column" help="Column from the dataset to perform the computation on."/>
        <param name="transformation" type="select" label="Transformation">
            <option value="log2">Log2</option>
            <option value="log10">Log10</option>
            <option value="ln">Ln</option>
            <option value="sqrt">Sqrt</option>
            <option value="exp">Exp</option>
            <option value="abs">Abs</option>
            <option value="floor">Floor</option>
            <option value="ceil">Ceil</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_dataset" format_source="input_dataset" label="${transformation} transform on ${on_string}">
            <change_format>
                <when input="input_dataset.ext" value="tsv" format="tabular" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_dataset" value="query.tabular" ftype="tabular"/>
            <param name="columns" value="1,3"/>
            <param name="transformation" value="ln"/>
            <output name="output_dataset" file="transform/query_log.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
This tool applies mathematical transformations to specified columns in a dataframe.

Inputs
------

- **Input Dataset**: The input dataset in CSV, TSV, tabular, or Parquet format.
- **Columns to Transform**: Select one or more columns from the dataset to transform. You can select columns by their header names.
- **Transformation**: The mathematical transformation to apply to the selected columns. Choose from log, log10, ln, sqrt, exp, abs, floor, or ceil.

Outputs
-------

- **Output Dataset**: The output dataset with the transformed columns.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3509134</citation>
        <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
    </citations>
</tool>