Mercurial > repos > bgruening > chemfp
comparison butina_clustering.xml @ 2:70b071de9bee draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:31:44 -0400 |
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children | 0d88631bb7de |
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1:43a9e7d9b24f | 2:70b071de9bee |
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1 <tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.2"> | |
2 <description>of molecular fingerprints</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.1p1">chemfp</requirement> | |
5 <requirement type="package" version="2.4.1">openbabel</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/butina_clustering.py' | |
10 -i '$infile' | |
11 -t $threshold | |
12 -o '$outfile' | |
13 -p \${GALAXY_SLOTS:-1} | |
14 ]]> | |
15 </command> | |
16 <inputs> | |
17 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> | |
18 <param name='threshold' type='float' value='0.8'/> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="tabular" name="outfile"/> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="infile" ftype="fps" value="targets.fps"/> | |
26 <param name='threshold' value='0.8' ></param> | |
27 <output name="outfile" ftype="tabular" file='Taylor-Butina_Clustering_on_data_q.txt'/> | |
28 </test> | |
29 </tests> | |
30 <help> | |
31 <![CDATA[ | |
32 | |
33 | |
34 .. class:: infomark | |
35 | |
36 **What this tool does** | |
37 | |
38 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. | |
39 | |
40 .. _chemfp: http://chemfp.com/ | |
41 | |
42 ----- | |
43 | |
44 .. class:: infomark | |
45 | |
46 **Input** | |
47 | |
48 | Molecular fingerprints in FPS format. | |
49 | Open Babel Fastsearch index is not supported. | |
50 | |
51 * Example:: | |
52 | |
53 - fingerprints in FPS format | |
54 | |
55 #FPS1 | |
56 #num_bits=881 | |
57 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
58 #software=CACTVS/unknown | |
59 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat | |
60 #date=2012-02-09T13:20:37 | |
61 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e | |
62 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009 | |
63 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e | |
64 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807 | |
65 ........ | |
66 | |
67 - Tanimoto threshold : 0.8 (between 0 and 1) | |
68 | |
69 ----- | |
70 | |
71 .. class:: infomark | |
72 | |
73 **Output** | |
74 | |
75 * Example:: | |
76 | |
77 0 true singletons | |
78 => | |
79 | |
80 0 false singletons | |
81 => | |
82 | |
83 1 clusters | |
84 55091849 has 12 other members | |
85 => 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823 | |
86 | |
87 | |
88 ]]> | |
89 </help> | |
90 <citations> | |
91 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> | |
92 </citations> | |
93 </tool> |