<tool id="openbabel_remIons" name="Remove counterions and fragments" 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@">2</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_remIons.py'
      -i '${infile}'
      -iformat '${infile.ext}'
      -o '${outfile}'
      $index
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <param name="index" type="boolean" checked="false" truevalue="-idx" falsevalue="" label="Output indexed tab-separated table?" help="Add an index column to the output file. This option will work only when input format is InChI or SMILES, otherwise it will be ignored." />
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="2_mol.smi"/>
            <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
        </test>
        <test>
            <param name="infile" ftype="inchi" value="na-sal.inchi"/>
            <output name="outfile" ftype="inchi" file="na-sal_obrmions.inchi" />
        </test>
        <test>
            <param name="infile" ftype="inchi" value="multiple.inchi"/>
            <param name="index" value="true"/>
            <output name="outfile" ftype="inchi" file="multiple_obrmions.inchi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Parses a multiple molecules file and deletes any counterions or fragments present.

-----

.. class:: warningmark

**Hint**

| For each molecule, all fragments except for the largest are deleted.
|
| Only molecules with more than 5 heavy atoms are parsed.


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