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1 <tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
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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="1.1p1">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>
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8 #if $method_opts.method_opts_selector == "chemfp":
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9 simsearch
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10 #if int($method_opts.knn) == 0:
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11 #set $k = 'all'
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12 ## count is only available if k nearest neighbor search is disabled
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13 $method_opts.counts
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14 #else:
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15 #set $k = int($method_opts.knn)
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16 #end if
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17
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18 -k $k
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19
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20 --threshold $method_opts.threshold
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21 --query-format fps
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22 --target-format fps
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23 -o "${outfile}"
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24
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25 ## build and search an in-memory data structure (faster for multiple queries)
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26 --memory
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27
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28 #if $method_opts.query_opts.query_opts_selector == "normal":
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29 -q "${method_opts.query_opts.query}"
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30 #else:
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31 --NxN
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32 #end if
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33
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34 "${method_opts.query_opts.targets}"
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35 #else:
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36 ## 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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37 ## 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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38 ## A workaround is to create a symlink with a proper file-extension.
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39 #import tempfile
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40 #set $temp_file = tempfile.NamedTemporaryFile()
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41 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
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42 $temp_file.close()
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43 ln -s $method_opts.query $temp_link;
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44 obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&1;
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45 rm $temp_link
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46 #end if
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47 </command>
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48 <inputs>
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49
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50 <conditional name="method_opts">
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51 <param name="method_opts_selector" type="select" label="Subject database/sequences">
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52 <option value="chemfp">Chemfp fingerprint file</option>
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53 <option value="obabel">OpenBabel Fastsearch Index</option>
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54 </param>
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55 <when value="chemfp">
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56 <conditional name="query_opts">
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57 <param name="query_opts_selector" type="select" label="Query Mode">
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58 <option value="normal">Query molecules are stores in a separate file</option>
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59 <option value="nxn">Target molecules are also queries (NxN)</option>
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60 </param>
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61 <when value="normal">
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62 <param name='query' type='data' format="fps" label='Query molecules'/>
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63 <param name='targets' type='data' format="fps" label='Target molecules'/>
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64 </when>
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65 <when value="nxn">
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66 <param name='targets' type='data' format="fps" label='Target moleculs'/>
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67 </when>
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68 </conditional>
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69 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
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70 <validator type="in_range" min="0" />
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71 </param>
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72 <param name='threshold' type='float' value='0.7' label='threshold' />
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73 <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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74 </when>
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75 <when value="obabel">
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76 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
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77 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
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78 <param name="threshold" type='float' label="threshold" value='0.7'/>
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79 </when>
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80 </conditional>
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81
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82 </inputs>
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83 <outputs>
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84 <data name="outfile" format="tabular" />
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="targets" ftype="fps" value="targets.fps"/>
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89 <param name="query" ftype="fps" value="q.fps"/>
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90 <param name="k" value='4'/>
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91 <param name="th" value='0.7'/>
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92 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
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93 </test>
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94 </tests>
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95 <help>
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96
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97
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98 .. class:: infomark
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99
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100 **What this tool does**
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101
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102 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
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103
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104 .. _chemfp: http://chemfp.com/
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105 .. _FastSearch: http://openbabel.org/wiki/FastSearch
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106
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107 -----
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108
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109 .. class:: infomark
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110
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111 **Cite**
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112
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113 | The chemfp_ project
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114 |
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115 | N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison - `Open Babel: An open chemical toolbox`_
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116
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117 .. _`Open Babel: An open chemical toolbox`: http://www.jcheminf.com/content/3/1/33
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118
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119
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120 </help>
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121 </tool>
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