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annotate simsearch.xml @ 17:e1e2746c8688 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:30:57 -0400
parents 987b62da416d
children f90b44d95052
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1 <tool id="ctb_simsearch" name="Similarity search" version="0.3">
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2 <description>of fingerprint data sets</description>
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3 <requirements>
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4 <requirement type="package" version="1.5">chemfp</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 #if $method_opts.method_opts_selector == "chemfp":
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9 ln -s '${method_opts.query_opts.targets}' ./targets.fps &&
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11 #if $method_opts.query_opts.query_opts_selector == "normal":
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12 ln -s '${method_opts.query_opts.query}' ./query.fps &&
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13 #end if
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15 simsearch
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16 #if int($method_opts.knn) == 0:
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17 #set $k = 'all'
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18 ## count is only available if k nearest neighbor search is disabled
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19 $method_opts.counts
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20 #else:
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21 #set $k = int($method_opts.knn)
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22 #end if
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23
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24 -k $k
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25 --threshold $method_opts.threshold
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26 -o ./output.fps
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27
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28 ## build and search an in-memory data structure (faster for multiple queries)
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29 --memory
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30
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31 #if $method_opts.query_opts.query_opts_selector == "normal":
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32 -q ./query.fps
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33 #else:
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34 --NxN
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35 #end if
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36
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37 ./targets.fps
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38 &&
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39 mv ./output.fps '${outfile}'
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40 #else:
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41 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
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42 ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
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43 ## A workaround is to create a symlink with a proper file-extension.
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44 ln -s '$method_opts.query' ./temp_query.$method_opts.query.ext
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45 obabel
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46 -i fs '$method_opts.fastsearch.files_path/molecule.fs'
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47 -S ./temp_query.$method_opts.query.ext
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48 -at${method_opts.threshold}
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49 -O '${outfile}'
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50 -osmi
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51 -aa
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52 #end if
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53 ]]>
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54 </command>
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55 <inputs>
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56 <conditional name="method_opts">
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57 <param name="method_opts_selector" type="select" label="Subject database/sequences">
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58 <option value="chemfp">Chemfp fingerprint file</option>
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59 <option value="obabel">OpenBabel Fastsearch Index</option>
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60 </param>
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61 <when value="chemfp">
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62 <conditional name="query_opts">
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63 <param name="query_opts_selector" type="select" label="Query mode">
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64 <option value="normal">Query molecules are stores in a separate file</option>
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65 <option value="nxn">Target molecules are also queries (NxN)</option>
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66 </param>
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67 <when value="normal">
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68 <param name='query' type='data' format="fps" label='Query molecules'/>
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69 <param name='targets' type='data' format="fps" label='Target molecules'/>
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70 </when>
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71 <when value="nxn">
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72 <param name='targets' type='data' format="fps" label='Target moleculs'/>
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73 </when>
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74 </conditional>
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75 <param name='knn' type='integer' value='0' label='Select the k nearest neighbors' help='0 means all neighbors'>
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76 <validator type="in_range" min="0" />
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77 </param>
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78 <param name='threshold' type='float' value='0.7' label='Minimum similarity score threshold' />
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79 <param name="counts" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Report counts (-c)" help="Is ignored if k nearest neighbor search is enabled" />
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80 </when>
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81 <when value="obabel">
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82 <param name="query" type='data' format="smi,mol,sdf,inchi" label="Query"/>
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83 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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84 <param name="threshold" type='float' label="Minimum similarity score threshold" value='0.7'/>
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85 </when>
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86 </conditional>
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87
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88 </inputs>
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89 <outputs>
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90 <data name="outfile" format="tabular" />
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="targets" ftype="fps" value="targets.fps"/>
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95 <param name="query" ftype="fps" value="q.fps"/>
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96 <param name="k" value='4'/>
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97 <param name="th" value='0.7'/>
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98 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
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99 </test>
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100 </tests>
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101 <help>
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102 <![CDATA[
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103
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104
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105 .. class:: infomark
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106
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107 **What this tool does**
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108
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109 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
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110
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111 .. _chemfp: http://chemfp.com/
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112 .. _FastSearch: http://openbabel.org/wiki/FastSearch
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114
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115 ]]>
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116 </help>
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117 <citations>
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118 <citation type="doi">10.1186/1758-2946-3-33</citation>
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119 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
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120 </citations>
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121 </tool>