<tool id="ctb_im_o3dalign" name="Open 3D Align" 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 $molquery ./molquery.sdf &&
        o3dAlign
            ./molquery.sdf  ##positional arg
            -i '$infile'
            -if sdf
            --qmolidx '$qmolidx'
            $crippen
            -n '$number'
            -t '$threshold'
            -a '$attempts'
            -r '$rmsd'
            -e '$emin'
            --meta
            -of sdf
            -o outp &>> $logfile &&
        cat outp_metrics.txt &>> $logfile &&
        gzip -d outp.sdf.gz
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
        <param name="molquery" type="data" format="sdf,mol" label="Mol query file" help="Mol file to align against"/>
        <param name="qmolidx" type="integer" value="1" label="Query molecule index" help="Query molecule index in SD-file if not the first"/>
        <param name="threshold" type="float" min="0" value="1" label="Threshold" help="Score cutoff relative to alignment of query to itself"/>
        <param name="number" type="integer" value="0" label="Number of conformers" help="Number of conformers to generate, if 0 then input structures are assumed to already be)"/>
        <param name="rmsd" type="float" min="0" value="1.0" label="RMSD Threshold" help="Prune RMSD threshold for excluding conformers"/>
        <param name="attempts" type="integer" min="0" value="0" label="Number of attempts" help="If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up."/>
        <param name="emin" type="integer" value="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/>
        <param name="crippen" type="boolean" label="Crippen" truevalue="--crippen" falsevalue="" help="Use Crippen (logP) contributions"/>
    </inputs>
    
    <expand macro="outputs" />
    
    <tests>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
            <param name="threshold" value="30" />
            <param name="number" value="2" />
            <output name="outfile">
                <assert_contents>
                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
                </assert_contents>
            </output>
            <output name="logfile">
                <assert_contents>
                    <has_text text="Perfect score: 0.0 134.34 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
            <param name="threshold" value="30" />
            <param name="number" value="2" />
            <param name="crippen" value="--crippen" />
            <output name="outfile">
                <assert_contents>
                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
                </assert_contents>
            </output>
            <output name="logfile">
                <assert_contents>
                    <has_text text="Perfect score: 0.0 114.13359999999997 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What this tool does**

Aligns molecules using RDKit's Open 3D Align.

.. class:: infomark

**Input**

| - Input file in `SDF Format`_

.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

 **Output**

SD-file of aligned compounds.

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