<tool id="ffindex_dbkit_extract" name="DBKit Extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
    <description>entries</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    dbkit_extract.py
        -l '$list'
        @db_source@
        -oi '$outindex'
        -od '$outdata'
        -g '$logfile'
    ]]>    </command>
    <inputs>
        <param name="list" type="data" format="tabular" label="List of entries" help="Select a tabular file containing the entries to be extracted." />
        <expand macro="db_source" />
        <expand macro="logfile" />
    </inputs>
    <outputs>
        <data format="ffindex" name="outindex" label="DBKit Extracted Index" />
        <data format="ffdata" name="outdata" label="DBKit Extracted Database" />
        <data format="txt" name="logfile" label="DBKit Extracted Log">
            <filter>logfile</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="list" value="create/pdb.tabular" />
            <conditional name="db_source">
                <param name="db_source_selector" value="history" />
                <param name="ffindex" value="merge/result.ffindex" />
                <param name="ffdata" value="merge/result.ffdata" />
            </conditional>
            <output name="outindex" file="merge/second.ffindex" />
            <output name="outdata" file="merge/second.ffdata" />
        </test>
        <test>
            <param name="list" value="create/pdb.tabular" />
            <conditional name="db_source">
                <param name="db_source_selector" value="indexed" />
                <param name="ffindex" value="merge" />
            </conditional>
            <output name="outindex" file="merge/second.ffindex" />
            <output name="outdata" file="merge/second.ffdata" />
        </test>
        <test>
            <param name="list" value="create/pdb_gz.tabular" />
            <conditional name="db_source">
                <param name="db_source_selector" value="indexed" />
                <param name="ffindex" value="first_gz" />
            </conditional>
            <output name="outindex" file="extract/third.ffindex" />
            <output name="outdata" file="extract/third.ffdata" />
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This database creation tool merges two pairs of ffindex/ffdata entries into a single ffindex/ffdata pair.
    ]]>    </help>
    <expand macro="citations" />
</tool>