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annotate chemfp_clustering/butina_clustering.xml @ 28:f874af3cf8df

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 00:54:07 +0200
parents 1868005213a1
children a2ba3431eca4
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7c84cfa515e0 ChemicalToolBoX update.
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1 <tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1">
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2 <description>of molecular fingerprints</description>
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3 <requirements>
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4 <requirement type="package" version="1.1p1">chemfp</requirement>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command interpreter='python'>
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8 butina_clustering.py
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9 -i $infile
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10 -t $threshold
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11 -o $outfile
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12 -p 4
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13 </command>
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14 <inputs>
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15 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
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16 <param name='threshold' type='float' value='0.8'/>
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="infile" ftype="fps" value="q.fps"/>
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24 <param name='threshold' value='0.8' ></param>
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25 <output name="outfile" ftype="tabular" file='Taylor-Butina_Clustering_on_data_q.txt'/>
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26 </test>
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27 </tests>
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28 <help>
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31 .. class:: infomark
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32
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33 **What this tool does**
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34
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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.
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36
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37 .. _chemfp: http://chemfp.com/
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39 -----
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41 .. class:: infomark
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42
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43 **Input**
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44
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45 | Molecular fingerprints in FPS format.
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46 | Open Babel Fastsearch index is not supported.
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47
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48 * Example::
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49
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50 - fingerprints in FPS format
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51
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52 #FPS1
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53 #num_bits=881
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54 #type=CACTVS-E_SCREEN/1.0 extended=2
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55 #software=CACTVS/unknown
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56 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
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57 #date=2012-02-09T13:20:37
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58 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
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59 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009
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60 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
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61 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807
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62 ........
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63
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64 - Tanimoto threshold : 0.8 (between 0 and 1)
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65
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66 -----
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67
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68 .. class:: infomark
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70 **Output**
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71
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72 * Example::
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74 0 true singletons
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75 =>
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77 0 false singletons
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78 =>
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79
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80 1 clusters
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81 55091849 has 12 other members
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82 => 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823
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84 -----
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86 .. class:: infomark
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87
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88 **Cite**
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90 The chemfp_ project from Andrew Dalke!
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92 .. _chemfp: http://chemfp.com/
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93
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94 </help>
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96 </tool>