annotate ob_remDuplicates.xml @ 14:b2569e22b40c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"

<tool id="openbabel_remDuplicates" name="Remove duplicated molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>from a library of compounds</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[
    obabel
      -i"${infile.ext}"
       "${infile}"
      -ocopy
      --unique "${descriptor}"
      -O "${outfile}"
      -e
]]>
    </command>
    <inputs>
        <expand macro="infile_all_types"/>
        <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
            <option value="inchi" selected="True">InChI (default)</option>
            <option value="cansmi">Canonical SMILES</option>
            <option value="cansmiNS">Canonical SMILES (without stereo)</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="output_like_input"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="smi" value="2_mol.smi"/>
                <param name="descriptor" value="inchi" />
            <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Filters a library of compounds and removes duplicated molecules.

-----

.. class:: warningmark

**Hint**

Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms.

-----

.. class:: infomark

**Input**

| - `InChI`_
| - `SMILES Format`_

.. _InChI: https://en.wikipedia.org/wiki/International_Chemical_Identifier
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

**Output**

Same as input format.


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