<tool id="query" name="Query" version="@TOOL_VERSION@">
    <macros>
        <token name="@TOOL_VERSION@">0.1</token>
        <xml name="formats">
            <option value="csv">csv</option>
            <option value="tsv">tsv</option>
            <option value="h5">h5</option>
            <option value="feather">feather</option>
            <option value="parquet">parquet</option>
            <option value="sqlite">sqlite</option>
        </xml>
        <xml name="internal_name" token_format="">
            <when value="@FORMAT@">
                <param name="name" type="text" help="Specify the format's internal name of the table."/>
            </when>
        </xml>
    </macros>

    <requirements>
        <requirement type="package">click</requirement>
        <requirement type="package">pyarrow</requirement>
        <requirement type="package">pytables</requirement>
        <requirement type="package">pandas</requirement>
        <requirement type="package">pandasql</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>

    <command><![CDATA[
        python '$__tool_directory__/query.py'
            $config
    ]]></command>

    <configfiles>
        <configfile name="config"><![CDATA[
            #def filetype(data):
                #if $data.is_of_type('h5')
                    #return 'hdf'
                #elif $data.is_of_type('csv')
                    #return 'csv'
                #elif $data.is_of_type('tsv', 'tabular')
                    #return 'tsv'
                #elif $data.is_of_type('feather', 'arrow')
                    #return 'feather'
                #elif $data.is_of_type('parquet')
                    #return 'parquet'
                #elif $data.is_of_type('sqlite')
                    #return 'sqlite'
                #end if
            #end def

            #set $config = {
                'tables': [
                    {
                        'path': str($table.file),
                        'name': str($table.name) if $table.name else 't{}'.format(str($index)),
                        'format': str($table.format) if $table.format else $filetype($table.file)
                    }
                    for $index, $table in enumerate($tables)
                ],
                'query': str($query),
                'result': {
                    'path': str($output),
                    'name': str($result.name) if str($result.format) in ('h5', 'hdf', 'sqlite') and $result.name else None,
                    'format': str($result.format)
                }
            }

            #import json
            #echo $json.dumps($config)
        ]]></configfile>
    </configfiles>

    <inputs>
        <repeat name="tables" title="Table">
            <param name="file" type="data" format="csv,tsv,h5,feather,parquet,sqlite" label="File"/>
            <param name="format" type="select" optional="true">
                <label>Force the file format</label>
                <help>Force a particular file format to get around formats unknown to Galaxy, ie. Parquet.</help>
                <expand macro="formats"/>
            </param>
            <param name="name" type="text" optional="true">
                <label>Table name</label>
                <help>Choose an unique name for the table which then you may use in the SQL Query. By default tables will be named as: t0, t1, ...</help>
            </param>
        </repeat>
        <param name="query" type="text" area="true">
            <label>SQL Query</label>
            <help>
                Type an arbitrary SQL SELECT to perform on the input tables. The input tables may be referred by their given names.
                An example query is SELECT employees.name AS employee, emails.value AS email FROM one JOIN b ON employees.id = emails.employee, provided that the input tables are named employees and emails.
            </help>
        </param>
        <conditional name="result">
            <param name="format" type="select">
                <label>SQL Query</label>
                <help>Specify the file format of the query result.</help>
                <expand macro="formats"/>
            </param>
            <expand macro="internal_name" format="h5"/>
            <expand macro="internal_name" format="sqlite"/>
        </conditional>
    </inputs>

    <outputs>
        <data name="output">
            <change_format>
                <when input="result.format" value="h5" format="h5"/>
                <when input="result.format" value="csv" format="csv"/>
                <when input="result.format" value="tsv" format="tsv"/>
                <when input="result.format" value="feather" format="feather"/>
                <when input="result.format" value="parquet" format="parquet"/>
                <when input="result.format" value="sqlite" format="sqlite"/>
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <repeat name="tables">
                <param name="file" value="a.csv" ftype="csv"/>
                <param name="name" value="a"/>
            </repeat>
            <repeat name="tables">
                <param name="file" value="b.csv" ftype="csv"/>
                <param name="name" value="b"/>
            </repeat>
            <param name="query" value="SELECT a.x AS ax, a.y AS ay, a.z AS az, b.x AS bx, b.y AS by, b.z AS bz FROM a JOIN b ON a.x = b.x"/>
            <conditional name="result">
                <param name="format" value="csv"/>
            </conditional>
            <output name="output" file="ab.csv" ftype="csv"/>
        </test>
    </tests>
</tool>