Mercurial > repos > bgruening > chemfp

annotate butina_clustering.xml @ 36:bcb3c078b2b4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit d786052cd04f8b25eb4aff80b1b9724f62031b61
author bgruening
date Sat, 20 May 2017 12:56:09 -0400
parents 73b8c87779ae
children 02e03ac072cf
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73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 <tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.2">
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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="2.4.1">openbabel</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/butina_clustering.py'
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10 -i '$infile'
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11 -t $threshold
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12 -o '$outfile'
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13 -p \${GALAXY_SLOTS:-1}
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
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18 <param name='threshold' type='float' value='0.8'/>
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" name="outfile"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="infile" ftype="fps" value="targets.fps"/>
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26 <param name='threshold' value='0.8' ></param>
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27 <output name="outfile" ftype="tabular" file='Taylor-Butina_Clustering_on_data_q.txt'/>
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28 </test>
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29 </tests>
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30 <help>
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31 <![CDATA[
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34 .. class:: infomark
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35
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36 **What this tool does**
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37
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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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.
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40 .. _chemfp: http://chemfp.com/
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42 -----
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43
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44 .. class:: infomark
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45
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46 **Input**
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47
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48 | Molecular fingerprints in FPS format.
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49 | Open Babel Fastsearch index is not supported.
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50
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51 * Example::
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52
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53 - fingerprints in FPS format
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54
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55 #FPS1
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56 #num_bits=881
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57 #type=CACTVS-E_SCREEN/1.0 extended=2
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58 #software=CACTVS/unknown
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59 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
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60 #date=2012-02-09T13:20:37
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61 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
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62 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009
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63 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
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64 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807
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65 ........
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66
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67 - Tanimoto threshold : 0.8 (between 0 and 1)
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68
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69 -----
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71 .. class:: infomark
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72
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73 **Output**
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74
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75 * Example::
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76
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77 0 true singletons
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78 =>
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80 0 false singletons
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81 =>
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83 1 clusters
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84 55091849 has 12 other members
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85 => 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823
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86
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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88 ]]>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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89 </help>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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90 <citations>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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92 </citations>
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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93 </tool>