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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:40:22 -0400
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1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.4">
2 <description>calculated with RDKit</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements>
5 <requirement type="package" version="2019.03.1">rdkit</requirement>
6
7 </requirements>
8 <command>
9 <![CDATA[
10 python '$__tool_directory__/rdkit_descriptors.py'
11 -i '${infile}'
12 --iformat '${infile.ext}'
13 -o '${outfile}'
14 $header
15 ]]>
16 </command>
17 <inputs>
18 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data"
19 help="In SDF or SMILES format"/>
20 <param name="header" type="boolean" label="Include the descriptor name as header"
21 truevalue="--header" falsevalue="" checked="false" />
22 </inputs>
23 <outputs>
24 <data format="tabular" name="outfile" />
25 </outputs>
26 <tests>
27 <test>
28 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
29 <param name="header" value="True" />
30 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
31 </test>
32 </tests>
33 <help>
34 <![CDATA[
35
36 .. class:: infomark
37
38 **What this tool does**
39
40 | RDKit is an open source toolkit for cheminformatics and machine learning.
41 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors.
42 |
43
44 +-----------------------------------+------------+
45 | Descriptor/Descriptor Family | Language |
46 +===================================+============+
47 | Gasteiger/Marsili Partial Charges | C++ |
48 +-----------------------------------+------------+
49 | BalabanJ | Python |
50 +-----------------------------------+------------+
51 | BertzCT | Python |
52 +-----------------------------------+------------+
53 | Ipc | Python |
54 +-----------------------------------+------------+
55 | HallKierAlpha | Python |
56 +-----------------------------------+------------+
57 | Kappa1 - Kappa3 | Python |
58 +-----------------------------------+------------+
59 | Chi0, Chi1 | Python |
60 +-----------------------------------+------------+
61 | Chi0n - Chi4n | Python |
62 +-----------------------------------+------------+
63 | Chi0v - Chi4v | Python |
64 +-----------------------------------+------------+
65 | MolLogP | C++ |
66 +-----------------------------------+------------+
67 | MolMR | C++ |
68 +-----------------------------------+------------+
69 | MolWt | C++ |
70 +-----------------------------------+------------+
71 | HeavyAtomCount | Python |
72 +-----------------------------------+------------+
73 | HeavyAtomMolWt | Python |
74 +-----------------------------------+------------+
75 | NHOHCount | C++ |
76 +-----------------------------------+------------+
77 | NOCount | C++ |
78 +-----------------------------------+------------+
79 | NumHAcceptors | C++ |
80 +-----------------------------------+------------+
81 | NumHDonors | C++ |
82 +-----------------------------------+------------+
83 | NumHeteroatoms | C++ |
84 +-----------------------------------+------------+
85 | NumRotatableBonds | C++ |
86 +-----------------------------------+------------+
87 | NumValenceElectrons | Python |
88 +-----------------------------------+------------+
89 | RingCount | C++ |
90 +-----------------------------------+------------+
91 | TPSA | C++ |
92 +-----------------------------------+------------+
93 | LabuteASA | C++ |
94 +-----------------------------------+------------+
95 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
96 +-----------------------------------+------------+
97 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
98 +-----------------------------------+------------+
99 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
100 +-----------------------------------+------------+
101 | EState_VSA1 - EState_VSA11 | Python |
102 +-----------------------------------+------------+
103 | VSA_EState1 - VSA_EState10 | Python |
104 +-----------------------------------+------------+
105 | Topliss fragments | Python |
106 +-----------------------------------+------------+
107
108 |
109 | A full list of the descriptors can be obtained here_.
110
111 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors
112
113 -----
114
115 .. class:: warningmark
116
117 **Hint**
118
119 Use the **cut columns from a table** tool to select just the desired descriptors.
120
121 -----
122
123 .. class:: infomark
124
125 **Input**
126
127 | - `SDF Format`_
128 | - `SMILES Format`_
129 | - `Corina MOL2`_
130
131 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
132 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
133 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
134
135 -----
136
137 .. class:: infomark
138
139 **Output**
140
141 Tabular file, where each descriptor (value) is shown in a separate column.
142
143
144 ]]>
145 </help>
146 <citations>
147 <citation type="bibtex">
148 @article{rdkit,
149 author = {Greg Landrum and others},
150 title = {RDKit: Open-source cheminformatics},
151 url ={http://www.rdkit.org}
152 }</citation>
153 </citations>
154 </tool>