annotate ob_remIons.xml @ 2:bf3b0107c0f4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 78ac0521d7df684e96c1b9c1ba2a17b02e681608

<tool id="openbabel_remIons" name="Remove counterions and fragments" version="@VERSION@.0">
    <description></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>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_remIons.py'
      -i '${infile}'
      -iformat '${infile.ext}'
      -o '${outfile}'
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
    </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>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

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

-----

.. class:: warningmark

**Hint**

| Only the **largest fragment** on every molecule is extracted.
|
| Only molecules with more than 5 heavy atoms are parsed.


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