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comparison simsearch.xml @ 0:52e5c0f2907f draft

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author bgruening
date Thu, 15 Aug 2013 03:36:37 -0400
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1 <tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
2 <description>of fingerprint data sets</description>
3 <requirements>
4 <requirement type="package" version="1.1p1">chemfp</requirement>
5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 </requirements>
7 <command>
8 #if $method_opts.method_opts_selector == "chemfp":
9 simsearch
10 #if int($method_opts.knn) == 0:
11 #set $k = 'all'
12 ## count is only available if k nearest neighbor search is disabled
13 $method_opts.counts
14 #else:
15 #set $k = int($method_opts.knn)
16 #end if
17
18 -k $k
19
20 --threshold $method_opts.threshold
21 --query-format fps
22 --target-format fps
23 -o "${outfile}"
24
25 ## build and search an in-memory data structure (faster for multiple queries)
26 --memory
27
28 #if $method_opts.query_opts.query_opts_selector == "normal":
29 -q "${method_opts.query_opts.query}"
30 #else:
31 --NxN
32 #end if
33
34 "${method_opts.query_opts.targets}"
35 #else:
36 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
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.
38 ## A workaround is to create a symlink with a proper file-extension.
39 #import tempfile
40 #set $temp_file = tempfile.NamedTemporaryFile()
41 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
42 $temp_file.close()
43 ln -s $method_opts.query $temp_link;
44 obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&#38;1;
45 rm $temp_link
46 #end if
47 </command>
48 <inputs>
49
50 <conditional name="method_opts">
51 <param name="method_opts_selector" type="select" label="Subject database/sequences">
52 <option value="chemfp">Chemfp fingerprint file</option>
53 <option value="obabel">OpenBabel Fastsearch Index</option>
54 </param>
55 <when value="chemfp">
56 <conditional name="query_opts">
57 <param name="query_opts_selector" type="select" label="Query Mode">
58 <option value="normal">Query molecules are stores in a separate file</option>
59 <option value="nxn">Target molecules are also queries (NxN)</option>
60 </param>
61 <when value="normal">
62 <param name='query' type='data' format="fps" label='Query molecules'/>
63 <param name='targets' type='data' format="fps" label='Target molecules'/>
64 </when>
65 <when value="nxn">
66 <param name='targets' type='data' format="fps" label='Target moleculs'/>
67 </when>
68 </conditional>
69 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
70 <validator type="in_range" min="0" />
71 </param>
72 <param name='threshold' type='float' value='0.7' label='threshold' />
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" />
74 </when>
75 <when value="obabel">
76 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
77 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
78 <param name="threshold" type='float' label="threshold" value='0.7'/>
79 </when>
80 </conditional>
81
82 </inputs>
83 <outputs>
84 <data name="outfile" format="tabular" />
85 </outputs>
86 <tests>
87 <test>
88 <param name="targets" ftype="fps" value="targets.fps"/>
89 <param name="query" ftype="fps" value="q.fps"/>
90 <param name="k" value='4'/>
91 <param name="th" value='0.7'/>
92 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
93 </test>
94 </tests>
95 <help>
96
97
98 .. class:: infomark
99
100 **What this tool does**
101
102 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
103
104 .. _chemfp: http://chemfp.com/
105 .. _FastSearch: http://openbabel.org/wiki/FastSearch
106
107 -----
108
109 .. class:: infomark
110
111 **Cite**
112
113 | The chemfp_ project
114 |
115 | N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison - `Open Babel: An open chemical toolbox`_
116
117 .. _`Open Babel: An open chemical toolbox`: http://www.jcheminf.com/content/3/1/33
118
119
120 </help>
121 </tool>