|
0
|
1 <tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.1">
|
|
|
2 <description>likeness calculator</description>
|
|
3
|
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>
|
|
0
|
4 <requirements>
|
|
|
5 <requirement type="package" version="1.4.1">np-likeness-scorer</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command>
|
|
|
8 java -jar \$JAVA_JAR_PATH/NPLikenessCalculator-1.4.1.jar
|
|
|
9 -in "${infile}"
|
|
|
10 -out "${outfile}"
|
|
|
11 #if $reconstruct_fragments:
|
|
|
12 -reconstructFragments true
|
|
|
13 -outFragments $outfragments
|
|
|
14 #end if
|
|
|
15 </command>
|
|
|
16 <stdio>
|
|
|
17 <exit_code range="1:" />
|
|
|
18 <exit_code range=":-1" />
|
|
|
19 </stdio>
|
|
|
20 <inputs>
|
|
|
21 <param format="sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/>
|
|
|
22 <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' />
|
|
|
23 </inputs>
|
|
|
24 <outputs>
|
|
|
25 <data format="sdf" name="outfile" />
|
|
|
26 <data format="tabular" name="outfragments">
|
|
|
27 <filter>reconstruct_fragments is True</filter>
|
|
|
28 </data>
|
|
|
29 </outputs>
|
|
|
30 <tests>
|
|
|
31 </tests>
|
|
|
32 <help>
|
|
|
33
|
|
|
34
|
|
|
35 .. class:: infomark
|
|
|
36
|
|
|
37 **INFO:** The more positive the score, the higher is the NP-likeness and vice versa.
|
|
|
38
|
|
|
39 .. image:: $PATH_TO_IMAGES/score_distribution.png
|
|
|
40
|
|
|
41
|
|
|
42 **What it is**
|
|
|
43
|
|
|
44 The `Natural-Product-Likeness Scorer`_ is an open-source, open-data re-implementation of
|
|
|
45 Peter Ertl’s previous work [2] and calculates a natural product-likeness score.
|
|
|
46
|
|
|
47 .. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/
|
|
|
48
|
|
|
49 -----
|
|
|
50
|
|
|
51
|
|
|
52 **Cite**
|
|
|
53 [1] KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl, Natural product-likeness score revisited:
|
|
|
54 an open-source, open-data implementation, BMC Bioinformatics 2012, 13:106
|
|
|
55
|
|
|
56 http://www.biomedcentral.com/1471-2105/13/106/abstract
|
|
|
57
|
|
|
58 [2] P Ertl, S Roggo, and A Schuffenhauer, Natural product-likeness score and its application for prioritization
|
|
|
59 of compound libraries., J. Chem. Inf. Model, 2008 vol. 48 (1) pp. 68-74
|
|
|
60
|
|
|
61 http://www.ncbi.nlm.nih.gov/pubmed/18034468
|
|
|
62
|
|
|
63 </help>
|
|
|
64 </tool>
|
