annotate rdkit_descriptors.xml @ 1:2f212f34b80c draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 9a3dc91fa984be18fabc0d968360634d787c9589

<tool id="ctb_rdkit_describtors" name="Descriptors" version="0.3">
    <description>calculated with RDKit</description>
    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
    <requirements>
        <requirement type="package" version="2016.03.3">rdkit</requirement>
    </requirements>
    <command>
<![CDATA[
        python '$__tool_directory__/rdkit_descriptors.py'
            -i '${infile}'
            --iformat '${infile.ext}'
            -o '${outfile}'
            $header
]]>
    </command>
    <inputs>
        <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data"
            help="In SD- or SMILES-format"/>
        <param name="header" type="boolean" label="Include the descriptor name as header"
            truevalue="--header" falsevalue="" checked="false" />
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" />
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype='sdf' value="CID_3037.sdf" />
            <param name="header" value="True" />
            <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

| RDKit is an open source toolkit for cheminformatics and machine learning.
| This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions.
|
| The table below shows a brief overview of the descriptors.
|

+-----------------------------------+------------+
|    Descriptor/Descriptor Family   |  Language  |
+===================================+============+
| Gasteiger/Marsili Partial Charges |     C++    |
+-----------------------------------+------------+
|            BalabanJ               |   Python   |
+-----------------------------------+------------+
|             BertzCT               |   Python   |
+-----------------------------------+------------+
|               Ipc                 |   Python   |
+-----------------------------------+------------+
|          HallKierAlpha            |   Python   |
+-----------------------------------+------------+
|         Kappa1 - Kappa3           |   Python   |
+-----------------------------------+------------+
|            Chi0, Chi1             |   Python   |
+-----------------------------------+------------+
|           Chi0n - Chi4n           |   Python   |
+-----------------------------------+------------+
|           Chi0v - Chi4v           |   Python   |
+-----------------------------------+------------+
|              MolLogP              |     C++    |
+-----------------------------------+------------+
|               MolMR               |     C++    |
+-----------------------------------+------------+
|               MolWt               |     C++    |
+-----------------------------------+------------+
|           HeavyAtomCount          |   Python   |
+-----------------------------------+------------+
|           HeavyAtomMolWt          |   Python   |
+-----------------------------------+------------+
|             NHOHCount             |     C++    |
+-----------------------------------+------------+
|              NOCount              |     C++    |
+-----------------------------------+------------+
|            NumHAcceptors          |     C++    |
+-----------------------------------+------------+
|             NumHDonors            |     C++    |
+-----------------------------------+------------+
|            NumHeteroatoms         |     C++    |
+-----------------------------------+------------+
|          NumRotatableBonds        |     C++    |
+-----------------------------------+------------+
|         NumValenceElectrons       |   Python   |
+-----------------------------------+------------+
|              RingCount            |     C++    |
+-----------------------------------+------------+
|                 TPSA              |     C++    |
+-----------------------------------+------------+
|              LabuteASA            |     C++    |
+-----------------------------------+------------+
|       PEOE_VSA1 - PEOE_VSA14      | Python/C++ |
+-----------------------------------+------------+
|         SMR_VSA1 - SMR_VSA10      | Python/C++ |
+-----------------------------------+------------+
|      SlogP_VSA1 - SlogP_VSA12     | Python/C++ |
+-----------------------------------+------------+
|     EState_VSA1 - EState_VSA11    |   Python   |
+-----------------------------------+------------+
|     VSA_EState1 - VSA_EState10    |   Python   |
+-----------------------------------+------------+
|           Topliss fragments       |   Python   |
+-----------------------------------+------------+

|
| A full list of the descriptors can be obtained here_.

.. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors

-----

.. class:: warningmark

**HINT**

Use the **cut columns from a table** tool to select just the desired descriptors.

-----

.. class:: infomark

**Input**

| - `SD-Format`_
| - `SMILES Format`_
| - `Corina MOL2`_

.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
.. _Corina MOL2: http://www.molecular-networks.com/products/corina

-----

.. class:: infomark

 **Output**

Tabularfile, where each descriptor (value) is shown in a seperate column.


]]>
    </help>
    <citations>
        <citation type="bibtex">
            @article{rdkit,
                author = {Greg Landrum},
                title = {RDKit: Open-source cheminformatics},
                url ={http://www.rdkit.org}
            }</citation>
    </citations>
</tool>