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annotate chemfp_clustering/nxn_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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1 <tool id="ctb_chemfp_nxn_clustering" name="NxN 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="1.7.0">numpy</requirement>
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5 <requirement type="package" version="1.1p1">chemfp</requirement>
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6 <requirement type="package" version="1.2.1">matplotlib</requirement>
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7 <requirement type="package" version="0.12.0">scipy</requirement>
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8 <requirement type="package" version="2.3.2">openbabel</requirement>
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9 </requirements>
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10 <command interpreter='python'>
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11 nxn_clustering.py
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12 -i $infile
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13 -t $threshold
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14 #if str($output_files) in ['both', 'image']:
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15 --cluster $image
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16 #end if
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17 #if str($output_files) in ['both', 'matrix']:
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18 --smatrix $smilarity_matrix
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19 #end if
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20 --oformat $oformat
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21 </command>
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22 <inputs>
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23 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
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24 <param name='threshold' type='float' value='0.0' />
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25 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
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26 <option value='png'>PNG</option>
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27 <option value='svg'>SVG</option>
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28 </param>
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29 <param name='output_files' type='select' format='text' label="Output options">
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30 <option value='both'>NxN matrix and Image</option>
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31 <option value='image'>Image</option>
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32 <option value='matrix'>NxN Matrix</option>
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33 </param>
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34
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35 </inputs>
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36 <outputs>
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37 <data name="image" type="data" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
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38 <filter>output_files == "both" or output_files == "image"</filter>
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39 <change_format>
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40 <when input="oformat" value="png" format="png"/>
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41 </change_format>
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42 </data>
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43 <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
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44 <filter>output_files == "both" or output_files == "matrix"</filter>
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45 </data>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="infile" ftype="fps" value="q.fps" />
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50 <param name='treshold' value='0.75' />
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51 <param name='output_files' value='image' />
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52 <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
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53 </test>
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54 </tests>
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55 <help>
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56
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57 .. class:: infomark
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58
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59 **What this tool does**
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60
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61 Generating hierarchical clusters and visualizing clusters with dendrograms.
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62 For the clustering and the fingerprint handling the chemfp_ project is used.
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64 .. _chemfp: http://chemfp.com/
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66 -----
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67
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68 .. class:: warningmark
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69
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70 **Hint**
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72 The plotting of the cluster image is sensible only with a small dataset.
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73
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74 -----
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76 .. class:: infomark
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77
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78 **Input**
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79
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80 Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported.
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81
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82 * Example::
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83
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84 - fingerprints in FPS format
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85
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86 #FPS1
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87 #num_bits=881
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88 #type=CACTVS-E_SCREEN/1.0 extended=2
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89 #software=CACTVS/unknown
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90 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
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91 #date=2012-02-09T13:20:37
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92 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
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93 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009
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94 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
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95 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807
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96 ........
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97
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98 - Tanimoto threshold : 0.8 (between 0 and 1)
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99
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100 -----
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101
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102 .. class:: informark
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103
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104 **Output**
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105
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106 * Example::
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107
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108 .. image:: $PATH_TO_IMAGES/NxN_clustering.png
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109
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110 -----
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111
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112 .. class:: infomark
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113
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114 **Cite**
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115
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116 The chemfp_ project from Andrew Dalke!
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117
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118 .. _chemfp: http://chemfp.com/
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119
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120 </help>
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121
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122 </tool>