view query.xml @ 1:55ca5d902f62 draft default tip

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/query commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"

<tool id="query" name="Query" version="@TOOL_VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <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>