<tool id="rem_complex" name="Remove coordination complexes" version="@TOOL_VERSION@+galaxy2"  profile="21.09">
    <description>Remove molecular coordination complexes from a list of structure representations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.5.3">pandas</requirement>
        <requirement type="package" version="3.1.1">openbabel</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        python  $__tool_directory__/rem_complex.py
        -i '${input}'
        -iformat '${input.ext}'
        -o '${output}' 
    ]]></command>

    <environment_variables>
        <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable>
    </environment_variables>
    
    <inputs>
        <param name="input" format="inchi,smi,csv" type="data" help="Accepted input formats: CSV, SMI, and InChI."/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="smi" value="input.smi" />
            <output name="output" ftype="smi" file="sample_output.smi"/>
        </test>
        <test>
            <param name="input" ftype="inchi" value="input.inchi"/>
            <output name="output" ftype="inchi" file="sample_output.inchi"/>
        </test>
        <test>
            <param name="input" ftype="csv" value="input.csv"/>
            <output name="output" ftype="csv" file="sample_output.csv"/>
        </test>
    </tests>
    <help>
        <![CDATA[
            @HELP@
        ]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
    </citations>
</tool>