<tool id="ctb_im_constrained_conf_gen" name="Constrained conformer generation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>with RDKit</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s $refmol ./refmol.sdf &&
        python -m pipelines.rdkit.constrained_conf_gen
            -i '$infile'
            -if sdf
            -r './refmol.sdf'
            #if $core_smi
                -c '$core_smi'
            #end if
            -n $number
            --refmolidx $refmolidx
            --meta
            -o outp
            -of sdf &>> $logfile &&
        cat outp_metrics.txt &>> $logfile &&
        gzip -dc outp.sdf.gz &>> outp.sdf || :
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
        <param name="refmol" type="data" format="sdf" label="SDF reference file" help="ABCD"/>
        <param name="refmolidx" type="integer" value="1" label="Reference molecule index" help="Index of the reference molecule index in the file, if not the first"/>
        <param name="number" type="integer" value="10" label="Number of conformers" help="Number of conformers to generate, if None then input structures are assumed to already be 3D')"/>
        <param name="core_smi" type="text" value="" label="Core substructure" help="If not specified - guessed using MCS"/>
    </inputs>
    
    <expand macro="outputs" />

    <tests>
        <test>
            <param name="infile" value="XChemReactionMaker1.sdf" ftype="sdf"/>
            <param name="refmol" value="ref_mol.sdf" ftype="sdf"/>
            <param name="number" value="2" />
            <output name="outfile" ftype="sdf" file="constrained_conf_gen_output1.sdf"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

This tool generates constrained conformers for a set of input molecules, using the chemistry toolkit RDKit.

-----

.. class:: infomark

**Input**

| - Molecules in `SDF format`_
| - Reference molecule in SDF format.

.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file


-----

.. class:: infomark

 **Output**

SD-file containing generated conformers.

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