Mercurial > repos > bgruening > chemfp
comparison chemfp_clustering/butina_clustering.xml @ 0:354d3c6bb894 draft
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author | bgruening |
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date | Thu, 15 Aug 2013 03:27:06 -0400 |
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children | 43a9e7d9b24f |
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1 <tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1"> | |
2 <description>of molecular fingerprints</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.1p1">chemfp</requirement> | |
5 <requirement type="package" version="2.3.2">openbabel</requirement> | |
6 </requirements> | |
7 <command interpreter='python'> | |
8 butina_clustering.py | |
9 -i $infile | |
10 -t $threshold | |
11 -o $outfile | |
12 -p 4 | |
13 </command> | |
14 <inputs> | |
15 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> | |
16 <param name='threshold' type='float' value='0.8'/> | |
17 </inputs> | |
18 <outputs> | |
19 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="infile" ftype="fps" value="q.fps"/> | |
24 <param name='threshold' value='0.8' ></param> | |
25 <output name="outfile" ftype="tabular" file='Taylor-Butina_Clustering_on_data_q.txt'/> | |
26 </test> | |
27 </tests> | |
28 <help> | |
29 | |
30 | |
31 .. class:: infomark | |
32 | |
33 **What this tool does** | |
34 | |
35 Unsupervised non-hierarchical clustering method based on the Taylor-Butina algorithm, which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. This tool is based on the chemfp_ project. | |
36 | |
37 .. _chemfp: http://chemfp.com/ | |
38 | |
39 ----- | |
40 | |
41 .. class:: infomark | |
42 | |
43 **Input** | |
44 | |
45 | Molecular fingerprints in FPS format. | |
46 | Open Babel Fastsearch index is not supported. | |
47 | |
48 * Example:: | |
49 | |
50 - fingerprints in FPS format | |
51 | |
52 #FPS1 | |
53 #num_bits=881 | |
54 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
55 #software=CACTVS/unknown | |
56 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat | |
57 #date=2012-02-09T13:20:37 | |
58 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e | |
59 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009 | |
60 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e | |
61 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807 | |
62 ........ | |
63 | |
64 - Tanimoto threshold : 0.8 (between 0 and 1) | |
65 | |
66 ----- | |
67 | |
68 .. class:: infomark | |
69 | |
70 **Output** | |
71 | |
72 * Example:: | |
73 | |
74 0 true singletons | |
75 => | |
76 | |
77 0 false singletons | |
78 => | |
79 | |
80 1 clusters | |
81 55091849 has 12 other members | |
82 => 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823 | |
83 | |
84 ----- | |
85 | |
86 .. class:: infomark | |
87 | |
88 **Cite** | |
89 | |
90 The chemfp_ project from Andrew Dalke! | |
91 | |
92 .. _chemfp: http://chemfp.com/ | |
93 | |
94 </help> | |
95 | |
96 </tool> |