<tool id="filter_orgmet_anorg" name="Filter organometallics and/or anorganics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from a library of compounds</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/filter_compounds.py'
      -i '${infile}'
      -o '${outfile}'
      $metorg
      $anorg
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="smi" label="Select input file" help="Currently only SMILES identifiers are allowed as an input."/>
        <param name="metorg" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Filter out organometallic compounds?" />
        <param name="anorg" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Filter out anorganic compounds?" />
    </inputs>
    <outputs>
	    <data format="smi" name="outfile"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="input_all.smi"/>
            <param name="metorg" value="true"/>
            <param name="anorg" value="true"/>	
            <output name="outfile" ftype="smi" file="output_all.smi" />
        </test>
        <test>
            <param name="infile" ftype="smi" value="input_all_table.smi"/>
            <param name="metorg" value="true"/>
            <param name="anorg" value="true"/>
            <output name="outfile" ftype="smi" file="output_all_table.smi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Filters organometallics (compounds containing atoms other than C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K) or anorganics (compounds without C). Input can be either list of SMILES identifiers or indexed table of SMILES (two tab-separated columns, first column is index, second columns is SMILES).

]]>
    </help>
</tool>