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comparison subsearch.xml @ 0:98e12cc1f3a8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:40:52 -0400
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children ab2b9d87b067
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-1:000000000000 0:98e12cc1f3a8
1 <tool id="openbabel_subsearch" name="Substructure Search" version="@VERSION@.0">
2 <description>of fingerprint data sets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="aggressive">
8 <![CDATA[
9
10 python '$__tool_directory__/subsearch.py'
11 -i '${query}'
12 --iformat '${query.ext}'
13 --fastsearch-index '${os.path.join($fastsearch.extra_files_path, 'molecule.fs')}'
14 -o '${outfile}'
15 --oformat $oformat
16 --max-candidates $max_candidates
17 --processors "\${GALAXY_SLOTS:-12}"
18
19 ]]>
20 </command>
21 <inputs>
22 <param name="query" type='data' format="tabular,smi,sdf,inchi,txt" label="query"/>
23 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index" help="The OpenBabel fastsearch index can be created with the convert tool."/>
24 <param name="max_candidates" type="integer" value="4000" label="The maximum number of candidates"/>
25 <param name='oformat' type='select' format='text' label="Output format.">
26 <option value='smi'>SMILES</option>
27 <option value='inchi'>InChI</option>
28 <option value='sdf'>SD-Files</option>
29 <option value='mol2'>mol2</option>
30 <option value='names'>Return the molecule names only</option>
31 </param>
32 </inputs>
33 <outputs>
34 <data format="smi" name="outfile">
35 <change_format>
36 <when input="oformat" value="inchi" format="inchi"/>
37 <when input="oformat" value="sdf" format="sdf"/>
38 <when input="oformat" value="mol2" format="mol2"/>
39 <when input="oformat" value="names" format="tabular"/>
40 </change_format>
41 </data>
42 </outputs>
43 <tests>
44 <test>
45 <param name="query" ftype="sdf" value="CID_2244.sdf"/>
46 <param name="fastsearch" value="ob_convert_on_CID2244_obfs.txt" ftype="obfs" >
47 <composite_data value='molecule.sdf' ftype="sdf"/>
48 <composite_data value='molecule.fs'/>
49 </param>
50 <param name="oformat" value="names" />
51 <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
52 </test>
53 </tests>
54 <help>
55 <![CDATA[
56
57 .. class:: infomark
58
59 **What this tool does**
60
61 Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.
62
63 .. _FastSearch: http://openbabel.org/wiki/FastSearch
64
65 -----
66
67 .. class:: infomark
68
69 **Input**
70
71 SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.
72
73
74 ]]>
75 </help>
76 <expand macro="citations"/>
77 </tool>