view filter/ob_remIons.xml @ 2:125da3a296ca draft default tip

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<tool id="ctb_remIons" name="Remove counterions and fragments" version="1.0">
    <description></description>
    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command interpreter="python">
<![CDATA[
    ob_remIons.py
      -i "${infile}"
      -iformat "${infile.ext}"
      -o "${outfile}"
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/>
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile"/>
    </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.

-----

.. class:: infomark

**Cite**

N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_

.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5

N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_

.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

]]>
    </help>
</tool>