<tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT">
    <description>database</description>
     <requirements>
        <requirement type="package" version="3.2">python-wget</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($source.type) == "false":
            mkdir -p inputs &&
            #for item in $source.inputs
                cp '${str(item)}' 'inputs/${item.element_identifier}' &&
            #end for
        #end if
        python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$source.url' -p 'inputs' -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."/>    
        <conditional name="source">
            <param name="type" type="boolean" label="Download from URL"/>
            <when value="true">
                <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>
                <param name="inputs" type="hidden"/>
            </when>
            <when value="false">
                <param name="url" type="hidden"/>
                <param name="inputs" type="data_collection" collection_type="list" label="Collection" help="Specify a collection containing the datasets."/>
            </when>
        </conditional>
        <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" />
            <conditional name="source">
                <param name="type" value="true"/>
                <param name="url" value="https://files.rcsb.org/download/" />
            </conditional>
            <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/first.ffindex" />
            <output name="database" file="create/first.ffdata" />
        </test>
        <test>
            <param name="input" value="create/sequences.tabular" />
            <conditional name="source">
                <param name="type" value="false"/>
                <param name="inputs">
                    <collection type="list">
                        <element name="NP_000282.1.hhr" value="create/NP_000282.1.hhr" />
                        <element name="NP_000290.2.hhr" value="create/NP_000290.2.hhr" />
                        <element name="NP_000548.2.hhr" value="create/NP_000548.2.hhr" />
                        <element name="NP_000836.2.hhr" value="create/NP_000836.2.hhr" />
                    </collection>
                </param>
            </conditional>
            <conditional name="advanced">
                <param name="type" value="false" />
            </conditional>
            <output name="index" file="create/sequences.ffindex" />
            <output name="database" file="create/sequences.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 size of every entry within the database file. The tool can also operate on collections.
    ]]></help>
</tool>