annotate remove_protonation_state.xml @ 13:b578d0c101cd draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"

<tool id="openbabel_remove_protonation_state" name="Remove protonation state" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>of every atom</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">1</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/remove_protonation_state.py'
        -i '$infile'
        -o '$outfile'
        --iformat '${infile.ext}'
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
            <output name="outfile" ftype="sdf" file="ob_remove_protonation_state.sdf" lines_diff="2" />
        </test>
        <test>
            <param name="infile" ftype="inchi" value="na-sal.inchi"/>
            <output name="outfile" ftype="inchi" file="ob_remove_protonation_state.inchi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Removes the protonation state of every atom.



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