view ob_addh.xml @ 12:43167f164076 draft

"planemo upload for repository commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:37:32 -0400
parents d2e6d682bcd0
children f697d9601273
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<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-->
        <token name="@GALAXY_VERSION@">0</token>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
        python $__tool_directory__/
            -i "${infile}"
            --iformat "${infile.ext}"
            -o "${outfile}"
            --pH "${pH_value}"
        <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"/>
        <expand macro="output_like_input"/>
            <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" />

.. 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


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

.. _SDF:


.. class:: warningmark


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


.. class:: infomark


Same output format as the input format.

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