Mercurial > repos > bgruening > chemfp
annotate simsearch.xml @ 4:685a138131f0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
author | bgruening |
---|---|
date | Sat, 20 May 2017 12:45:01 -0400 |
parents | 892811a1f12c |
children |
rev | line source |
---|---|
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
1 <tool id="ctb_simsearch" name="Similarity Search" version="0.2"> |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
2 <description>of fingerprint data sets</description> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
3 <requirements> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
4 <requirement type="package" version="1.1p1">chemfp</requirement> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
5 </requirements> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
6 <command> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
7 <![CDATA[ |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
8 #if $method_opts.method_opts_selector == "chemfp": |
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
9 ln -s '${method_opts.query_opts.targets}' ./targets.fps && |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
10 |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
11 #if $method_opts.query_opts.query_opts_selector == "normal": |
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
12 ln -s '${method_opts.query_opts.query}' ./query.fps && |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
13 #end if |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
14 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
15 simsearch |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
16 #if int($method_opts.knn) == 0: |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
17 #set $k = 'all' |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
18 ## count is only available if k nearest neighbor search is disabled |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
19 $method_opts.counts |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
20 #else: |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
21 #set $k = int($method_opts.knn) |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
22 #end if |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
23 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
24 -k $k |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
25 --threshold $method_opts.threshold |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
26 -o ./output.fps |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
27 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
28 ## build and search an in-memory data structure (faster for multiple queries) |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
29 --memory |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
30 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
31 #if $method_opts.query_opts.query_opts_selector == "normal": |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
32 -q ./query.fps |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
33 #else: |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
34 --NxN |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
35 #end if |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
36 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
37 ./targets.fps |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
38 && |
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
39 mv ./output.fps '${outfile}' |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
40 #else: |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
41 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that. |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
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. |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
43 ## A workaround is to create a symlink with a proper file-extension. |
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
44 ln -s '$method_opts.query' ./temp_query.$method_opts.query.ext |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
45 obabel |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
46 -i fs '$method_opts.fastsearch.files_path/molecule.fs' |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
47 -S ./temp_query.$method_opts.query.ext |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
48 -at${method_opts.threshold} |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
49 -O '${outfile}' |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
50 -osmi |
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
51 -aa |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
52 #end if |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
53 ]]> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
54 </command> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
55 <inputs> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
56 <conditional name="method_opts"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
57 <param name="method_opts_selector" type="select" label="Subject database/sequences"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
58 <option value="chemfp">Chemfp fingerprint file</option> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
59 <option value="obabel">OpenBabel Fastsearch Index</option> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
60 </param> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
61 <when value="chemfp"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
62 <conditional name="query_opts"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
63 <param name="query_opts_selector" type="select" label="Query Mode"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
64 <option value="normal">Query molecules are stores in a separate file</option> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
65 <option value="nxn">Target molecules are also queries (NxN)</option> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
66 </param> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
67 <when value="normal"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
68 <param name='query' type='data' format="fps" label='Query molecules'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
69 <param name='targets' type='data' format="fps" label='Target molecules'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
70 </when> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
71 <when value="nxn"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
72 <param name='targets' type='data' format="fps" label='Target moleculs'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
73 </when> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
74 </conditional> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
75 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
76 <validator type="in_range" min="0" /> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
77 </param> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
78 <param name='threshold' type='float' value='0.7' label='threshold' /> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
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" /> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
80 </when> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
81 <when value="obabel"> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
82 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
83 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
84 <param name="threshold" type='float' label="threshold" value='0.7'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
85 </when> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
86 </conditional> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
87 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
88 </inputs> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
89 <outputs> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
90 <data name="outfile" format="tabular" /> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
91 </outputs> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
92 <tests> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
93 <test> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
94 <param name="targets" ftype="fps" value="targets.fps"/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
95 <param name="query" ftype="fps" value="q.fps"/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
96 <param name="k" value='4'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
97 <param name="th" value='0.7'/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
98 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
99 </test> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
100 </tests> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
101 <help> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
102 <![CDATA[ |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
103 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
104 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
105 .. class:: infomark |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
106 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
107 **What this tool does** |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
108 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
109 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index. |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
110 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
111 .. _chemfp: http://chemfp.com/ |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
112 .. _FastSearch: http://openbabel.org/wiki/FastSearch |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
113 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
114 |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
115 ]]> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
116 </help> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
117 <citations> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
118 <citation type="doi">10.1186/1758-2946-3-33</citation> |
4
685a138131f0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
3
diff
changeset
|
119 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> |
3
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
120 </citations> |
892811a1f12c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff
changeset
|
121 </tool> |