<tool id="prepare_ligands_for_docking" name="Prepare ligands for docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
	    mkdir output && obabel -i '${ligands.ext}' -o '$oformat' -O 'output/molecule.$oformat' -m '$ligands' $gen3d -p $ph_value
    ]]></command>
    <inputs>
        <param type="data" name="ligands" format="sdf,mol2,inchi,smi" label="The ligands which need to be prepared" help="Input in SDF, MOL2, InChi or SMILES format." />
        <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
        <param name="gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
        <param name="oformat" type="select" label="Output format" >
            <option value="pdb">PDB</option>
            <option value="pdbqt">PDBQT</option>
            <option value="mol">MOL</option>
            <option value="mol2">MOL2</option>
        </param>
    </inputs>
    <outputs>
        <collection name="file_outputs" type="list" label="Prepared ligands" >
			<discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
            <param name="oformat" value="pdbqt"/>
            <param name="ph_value" value="7.4"/>
            <output_collection name="file_outputs" type="list" count="10">
                <element name="molecule1" file="ob_prepare_ligands1.pdbqt" />
                <element name="molecule2" file="ob_prepare_ligands2.pdbqt" />
                <!-- we check only the first 2 -->
            </output_collection>
        </test>
        <test>
            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
            <param name="oformat" value="mol2"/>
            <param name="ph_value" value="7.4"/>
            <output_collection name="file_outputs" type="list" count="10">
                <element name="molecule1" file="ob_prepare_ligands1.mol2" />
                <element name="molecule2" file="ob_prepare_ligands2.mol2" />
                <!-- we check only the first 2 -->
            </output_collection>
        </test>
        <test>
            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
            <param name="oformat" value="mol"/>
            <param name="ph_value" value="7.4"/>
            <output_collection name="file_outputs" type="list" count="10">
                <!-- just check the count -->
            </output_collection>
        </test>
        <test>
            <param name="ligands" ftype="sdf" value="ob_prepare_ligands.sdf"/>
            <param name="oformat" value="pdb"/>
            <param name="ph_value" value="7.4"/>
            <output_collection name="file_outputs" type="list" count="10">
                <!-- just check the count -->
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does?**

This tool uses OpenBabel to convert an input molecule file, typically a SD file, to individual output molecule files in pdbqt, pdb, 
mol or mol2 formats. There is one output file for each record in the input.
Protonation is performed at a specified pH and 3D coordinates can optionally be generated. 3D coordinate generation should be used when 
the docking program requires 3D structures and the input is not 3D.

The most typical usage is to process a set of ligands in a SD file that will be docked by VINA. In this case the pdbqt output format should
be used, and the resulting collection of molecules can be used as input by VINA.

**Input**

Molecules such as an SD file dataset in history.

**Output**

A collection of individual molecule files in the specified format.

    ]]></help>
    <expand macro="citations"/>
</tool>