--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdkit_descriptors.xml	Tue May 07 13:40:22 2019 -0400
@@ -0,0 +1,154 @@
+<tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.4">
+    <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="2019.03.1">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 SDF 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 tool calculates various molecular descriptors for the input data. 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**
+
+| - `SDF Format`_
+| - `SMILES Format`_
+| - `Corina MOL2`_
+
+.. _SDF 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**
+
+Tabular file, where each descriptor (value) is shown in a separate column.
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @article{rdkit,
+                author = {Greg Landrum and others},
+                title = {RDKit: Open-source cheminformatics},
+                url ={http://www.rdkit.org}
+            }</citation>
+    </citations>
+</tool>