<tool id="rdconf" name="RDConf: Low-energy ligand conformer search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using RDKit</description>
    <macros>
        <token name="@TOOL_VERSION@">2020.03.4</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
      <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rdkit</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/rdconf.py'
            '$infile'
            --maxconfs '$CNT'
            --sample_multiplier '$N'
            --seed '$s'
            --rms_threshold '$R'
            --energy_window '$E'
            $mmff
            $nomin
            $etkdg
            '$outfile'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="smi" label="Input file" help="Input file in SMILES format."/>
        <param name="CNT" type="integer"  value="20" label="Maximum number of conformers to generate per molecule"/>
        <param name="N" type="integer" value="1" label="Sample an integer multiple of the maximum conformer value and choose the conformers with lowest energy"/>
        <param name="s" type="integer" value="9162006" label="Random seed"/>
        <param name="R" type="float" value="0.7" min="0" label="RMSD threshold" help="If a conformer is too similar to those already generated (below the RMSD threshold), it is discarded and regenerated."/>
        <param name="E" type="float" value="10" label="Energy window threshold (kcal/mol)."/>
        <param name="mmff" type="boolean" value="" truevalue="--mmff" falsevalue="" label="Use MMFF forcefield (default UFF)"/>
        <param name="nomin" type="boolean" value="" truevalue="--nomin" falsevalue="" label="Skip minimization" help="Not recommended"/>
        <param name="etkdg" type="boolean" value="" truevalue="--etkdg" falsevalue="" label="Use new ETKDG knowledge-based method (default distance geometry)"/>
    </inputs>

    <outputs>
        <data name="outfile" format="sdf" label="Output for ${tool.name}"/>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="staurosporine.smi" ftype="smi"/>
            <param name="CNT" value="100"/>
            <param name="N" value="1"/>
            <param name="s" value="100"/>
            <param name="R" value="0.7"/>
            <param name="E" value="10"/>                       
            <param name="mmff" value="--mmff" />
            <param name="nomin" value="--nomin" />
            <param name="etkdg" value="--etkdg" />
            <output name="outfile" ftype="sdf" file="rdconf_output.sdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**


This tool generates low-energy conformers for a set of input molecules, using the chemistry toolkit RDKit. It is based on a script written by David Koes.

-----

.. class:: infomark

**Input**

| - Molecules in `SMI format`_
| - A number of other parameters can be set; the most important include the number of conformers (default 20) to generate and the minimum RMSD difference (default 0.7) between them.

.. _SMI format: https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

-----

.. class:: infomark

**Output**

`SD-file`_ containing generated conformers.

.. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file

]]></help>
    <citations>
        <citation type="bibtex">
            @article{rdkit,
                author = {Greg Landrum and others},
                title = {RDKit: Open-source cheminformatics},
                url ={http://www.rdkit.org}
            }</citation>
                    <citation type="bibtex">
            @article{rdconf,
                author = {David Koes},
                title = {RDConf: Low-energy ligand conformer search},
                url ={https://github.com/dkoes/rdkit-scripts}
            }</citation>
    </citations>
</tool>