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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 9a3dc91fa984be18fabc0d968360634d787c9589
author | bgruening |
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date | Wed, 24 May 2017 09:51:36 -0400 |
parents | d7ea4e8cb1f3 |
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<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>