Mercurial > repos > bgruening > ctb_rdkit_describtors
diff rdkit_descriptors.xml @ 0:d7ea4e8cb1f3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 12:41:19 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rdkit_descriptors.xml Sat May 20 12:41:19 2017 -0400 @@ -0,0 +1,155 @@ +<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>