<tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT">
    <description>database generator</description>
    <command detect_errors="exit_code"><![CDATA[
        mkdir temp &&
        python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$url' -t 'temp' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension'
    ]]></command>
    <inputs>
        <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/>
        <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
            <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
        </param>
        <conditional name="advanced">
            <param name="type" type="boolean" label="Identifier Formatting Options" />
            <when value="true">        
                <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/>
                <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)."/>
                <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional).">
                    <option value="">Unformatted</option>
                    <option value="lower">Lower</option>
                    <option value="upper">Upper</option>
                </param>
            </when>
            <when value="false">
                <param name="idextension" type="hidden" value="" />
                <param name="idlength" type="hidden" value="0" />
                <param name="idcase" type="hidden" value="" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="ffindex" name="index" label="DBKit Index"/>
        <data format="ffdata" name="database" label="DBKit Database" />
        <data format="txt" name="log" label="DBKit Log" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="create/chains.tabular" />
            <param name="url" value="https://files.rcsb.org/download/" />
            <conditional name="advanced">
                <param name="type" value="true" />
                <param name="idextension" value="pdb" />
                <param name="idlength" value="4" />
                <param name="idcase" value="lower" />
            </conditional>
            <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
            <output name="index" file="create/index.ffindex" />
            <output name="database" file="create/data.ffdata" />
        </test>
    </tests>
    <help><![CDATA[
This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
generated indicating the start and end of every entry within the database file.
    ]]></help>
</tool>