<tool id="openbabel_addh" name="Add hydrogen atoms" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>at a certain pH value</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@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
<![CDATA[
        python $__tool_directory__/ob_addh.py
            -i "${infile}"
            --iformat "${infile.ext}"
            -o "${outfile}"
            $polar
            --pH "${pH_value}"
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only (i.e. not to carbon atoms)"/>
        <param name="pH_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="CID_2244.can" ftype="smi" />
            <param name="polar" value="--polar" />
            <param name="pH_value" value="7.4" />
            <output name="outfile" file="CID_2244_addh.can" ftype="smi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Parses a molecular file and adds hydrogen atoms at a user-defined pH value.

* Protocol::

	1. The hydrogen atoms included in the input molecule are deleted.
	2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.

-----

.. class:: infomark

**Input**

3D format files are required, e.g. SDF_

.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file

-----

.. class:: warningmark

**Hint**

To avoid possible crashes, only molecules with more than five heavy atoms are parsed.

-----

.. class:: infomark

**Output**

Same output format as the input format.


]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1186/1752-153X-2-5</citation>
    </expand>
</tool>