simsearch: simsearch.xml annotate

annotate simsearch.xml @ 14:47d2bf691908

ChemicalToolBoX update.

author	Bjoern Gruening <bjoern.gruening@gmail.com>
date	Sun, 02 Jun 2013 19:54:51 +0200
parents	dbe9c82028d1
children	b4eaf75cac77

rev	line source
13 dbe9c82028d1 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 12 diff changeset	1 <tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
0 b4cbee77896d Uploaded bgruening parents: diff changeset	2 <description>of fingerprint data sets</description>
b4cbee77896d Uploaded bgruening parents: diff changeset	3 <requirements>
b4cbee77896d Uploaded bgruening parents: diff changeset	4 <requirement type="package" version="1.1p1">chemfp</requirement>
7 980199050694 Uploaded bgruening parents: 3 diff changeset	5 <requirement type="package" version="2.3.2">openbabel</requirement>
0 b4cbee77896d Uploaded bgruening parents: diff changeset	6 </requirements>
b4cbee77896d Uploaded bgruening parents: diff changeset	7 <command>
b4cbee77896d Uploaded bgruening parents: diff changeset	8 #if $method_opts.method_opts_selector == "chemfp":
12 526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	9 simsearch
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	10 #if int($method_opts.knn) == 0:
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	11 #set $k = 'all'
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	12 ## count is only available if k nearest neighbor search is disabled
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	13 $method_opts.counts
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	14 #else:
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	15 #set $k = int($method_opts.knn)
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	16 #end if
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	17
12 526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	18 -k $k
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	19
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	20 --threshold $method_opts.threshold
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	21 --query-format fps
12 526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	22 --target-format fps
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	23 -o "${outfile}"
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	24
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	25 ## build and search an in-memory data structure (faster for multiple queries)
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	26 --memory
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	27
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	28 #if $method_opts.query_opts.query_opts_selector == "normal":
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	29 -q "${method_opts.query_opts.query}"
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	30 #else:
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	31 --NxN
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	32 #end if
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	33
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	34 "${method_opts.query_opts.targets}"
0 b4cbee77896d Uploaded bgruening parents: diff changeset	35 #else:
b4cbee77896d Uploaded bgruening parents: diff changeset	36 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
b4cbee77896d Uploaded bgruening parents: diff changeset	37 ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
b4cbee77896d Uploaded bgruening parents: diff changeset	38 ## A workaround is to create a symlink with a proper file-extension.
b4cbee77896d Uploaded bgruening parents: diff changeset	39 #import tempfile
b4cbee77896d Uploaded bgruening parents: diff changeset	40 #set $temp_file = tempfile.NamedTemporaryFile()
b4cbee77896d Uploaded bgruening parents: diff changeset	41 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
b4cbee77896d Uploaded bgruening parents: diff changeset	42 $temp_file.close()
b4cbee77896d Uploaded bgruening parents: diff changeset	43 ln -s $method_opts.query $temp_link;
b4cbee77896d Uploaded bgruening parents: diff changeset	44 obabel -i fs "${os.path.join($method_opts.fastsearch.extra_files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&1;
b4cbee77896d Uploaded bgruening parents: diff changeset	45 rm $temp_link
b4cbee77896d Uploaded bgruening parents: diff changeset	46 #end if
b4cbee77896d Uploaded bgruening parents: diff changeset	47 </command>
b4cbee77896d Uploaded bgruening parents: diff changeset	48 <inputs>
b4cbee77896d Uploaded bgruening parents: diff changeset	49
b4cbee77896d Uploaded bgruening parents: diff changeset	50 <conditional name="method_opts">
b4cbee77896d Uploaded bgruening parents: diff changeset	51 <param name="method_opts_selector" type="select" label="Subject database/sequences">
b4cbee77896d Uploaded bgruening parents: diff changeset	52 <option value="chemfp">Chemfp fingerprint file</option>
b4cbee77896d Uploaded bgruening parents: diff changeset	53 <option value="obabel">OpenBabel Fastsearch Index</option>
b4cbee77896d Uploaded bgruening parents: diff changeset	54 </param>
b4cbee77896d Uploaded bgruening parents: diff changeset	55 <when value="chemfp">
12 526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	56 <conditional name="query_opts">
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	57 <param name="query_opts_selector" type="select" label="Query Mode">
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	58 <option value="normal">Query molecules are stores in a separate file</option>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	59 <option value="nxn">Target molecules are also queries (NxN)</option>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	60 </param>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	61 <when value="normal">
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	62 <param name='query' type='data' format="fps" label='Query molecules'/>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	63 <param name='targets' type='data' format="fps" label='Target molecules'/>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	64 </when>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	65 <when value="nxn">
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	66 <param name='targets' type='data' format="fps" label='Target moleculs'/>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	67 </when>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	68 </conditional>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	69 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	70 <validator type="in_range" min="0" />
526f6e88fbe7 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 7 diff changeset	71 </param>
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	72 <param name='threshold' type='float' value='0.7' label='threshold' />
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	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" />
0 b4cbee77896d Uploaded bgruening parents: diff changeset	74 </when>
b4cbee77896d Uploaded bgruening parents: diff changeset	75 <when value="obabel">
b4cbee77896d Uploaded bgruening parents: diff changeset	76 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
b4cbee77896d Uploaded bgruening parents: diff changeset	77 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
b4cbee77896d Uploaded bgruening parents: diff changeset	78 <param name="threshold" type='float' label="threshold" value='0.7'/>
b4cbee77896d Uploaded bgruening parents: diff changeset	79 </when>
b4cbee77896d Uploaded bgruening parents: diff changeset	80 </conditional>
b4cbee77896d Uploaded bgruening parents: diff changeset	81
b4cbee77896d Uploaded bgruening parents: diff changeset	82 </inputs>
b4cbee77896d Uploaded bgruening parents: diff changeset	83 <outputs>
b4cbee77896d Uploaded bgruening parents: diff changeset	84 <data name="outfile" format="tabular" />
b4cbee77896d Uploaded bgruening parents: diff changeset	85 </outputs>
b4cbee77896d Uploaded bgruening parents: diff changeset	86 <tests>
b4cbee77896d Uploaded bgruening parents: diff changeset	87 <test>
b4cbee77896d Uploaded bgruening parents: diff changeset	88 <param name="targets" ftype="fps" value="targets.fps"/>
b4cbee77896d Uploaded bgruening parents: diff changeset	89 <param name="query" ftype="fps" value="q.fps"/>
b4cbee77896d Uploaded bgruening parents: diff changeset	90 <param name="k" value='4'/>
b4cbee77896d Uploaded bgruening parents: diff changeset	91 <param name="th" value='0.7'/>
b4cbee77896d Uploaded bgruening parents: diff changeset	92 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
b4cbee77896d Uploaded bgruening parents: diff changeset	93 </test>
b4cbee77896d Uploaded bgruening parents: diff changeset	94 </tests>
b4cbee77896d Uploaded bgruening parents: diff changeset	95 <help>
b4cbee77896d Uploaded bgruening parents: diff changeset	96
b4cbee77896d Uploaded bgruening parents: diff changeset	97
b4cbee77896d Uploaded bgruening parents: diff changeset	98 What it does
b4cbee77896d Uploaded bgruening parents: diff changeset	99
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	100 Similarity search of compounds using fingerprint data sets. Depending on the input either chemfp_ of `Open Babel`_ is used.
0 b4cbee77896d Uploaded bgruening parents: diff changeset	101
b4cbee77896d Uploaded bgruening parents: diff changeset	102
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	103 References
0 b4cbee77896d Uploaded bgruening parents: diff changeset	104
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	105 Please reference the `Open Babel`_ or the chemfp_ project.
0 b4cbee77896d Uploaded bgruening parents: diff changeset	106
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	107 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	108 The Open Babel Package http://openbabel.sourceforge.net/
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	109
0 b4cbee77896d Uploaded bgruening parents: diff changeset	110
14 47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	111 .. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	112 .. _chemfp: http://chemfp.com/
47d2bf691908 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 13 diff changeset	113 .. _`Open Babel`: http://openbabel.org/
0 b4cbee77896d Uploaded bgruening parents: diff changeset	114
b4cbee77896d Uploaded bgruening parents: diff changeset	115 </help>
b4cbee77896d Uploaded bgruening parents: diff changeset	116 </tool>

Mercurial > repos > bgruening > simsearch

annotate simsearch.xml @ 14:47d2bf691908