view rdkit_descriptors.xml @ 3:77b168565931

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<tool id="ctb_rdkit_describtors" name="Descriptors" version="0.1">
    <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="2012_12_1">rdkit</requirement>
    </requirements>
    <command interpreter="python">rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&#38;1</command>
    <inputs>
        <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
        <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>
    </tests>
    <help>

.. class:: infomark

**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data

-----

**Example**

- Input file::

    - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file)
    - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)

- Result::


http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
http://rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html


-----


**Cite**

Greg Landrum
[1] RDKit: Open-source cheminformatics; http://www.rdkit.org


    </help>
</tool>