simsearch: simsearch.xml annotate

annotate simsearch.xml @ 3:9f1a8df0b437 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

author	bgruening
date	Tue, 28 Jul 2020 08:47:23 -0400
parents	497254c6c09e
children	425469deb136

rev	line source
3 9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	1 <tool id="ctb_simsearch" name="Similarity search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	2 <description>of fingerprint data sets with chemfp</description>
9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	3 <macros>
9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	4 <token name="@TOOL_VERSION@">1.6</token>
9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	5 <token name="@GALAXY_VERSION@">0</token>
9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	6 </macros>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	7 <requirements>
3 9f1a8df0b437 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0" bgruening parents: 2 diff changeset	8 <requirement type="package" version="1.6">chemfp</requirement>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	9 </requirements>
52e5c0f2907f Uploaded bgruening parents: diff changeset	10 <command>
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	11 <![CDATA[
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	12 #if $method_opts.method_opts_selector == "chemfp":
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	13 ln -s '${method_opts.query_opts.targets}' ./targets.fps &&
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	14
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	15 #if $method_opts.query_opts.query_opts_selector == "normal":
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	16 ln -s '${method_opts.query_opts.query}' ./query.fps &&
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	17 #end if
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	18
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	19 simsearch
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	20 #if int($method_opts.knn) == 0:
52e5c0f2907f Uploaded bgruening parents: diff changeset	21 #set $k = 'all'
52e5c0f2907f Uploaded bgruening parents: diff changeset	22 ## count is only available if k nearest neighbor search is disabled
52e5c0f2907f Uploaded bgruening parents: diff changeset	23 $method_opts.counts
52e5c0f2907f Uploaded bgruening parents: diff changeset	24 #else:
52e5c0f2907f Uploaded bgruening parents: diff changeset	25 #set $k = int($method_opts.knn)
52e5c0f2907f Uploaded bgruening parents: diff changeset	26 #end if
52e5c0f2907f Uploaded bgruening parents: diff changeset	27
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	28 -k $k
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	29 --threshold $method_opts.threshold
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	30 -o ./output.fps
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	31
52e5c0f2907f Uploaded bgruening parents: diff changeset	32 ## build and search an in-memory data structure (faster for multiple queries)
52e5c0f2907f Uploaded bgruening parents: diff changeset	33 --memory
52e5c0f2907f Uploaded bgruening parents: diff changeset	34
52e5c0f2907f Uploaded bgruening parents: diff changeset	35 #if $method_opts.query_opts.query_opts_selector == "normal":
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	36 -q ./query.fps
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	37 #else:
52e5c0f2907f Uploaded bgruening parents: diff changeset	38 --NxN
52e5c0f2907f Uploaded bgruening parents: diff changeset	39 #end if
52e5c0f2907f Uploaded bgruening parents: diff changeset	40
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	41 ./targets.fps
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	42 &&
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	43 mv ./output.fps '${outfile}'
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	44 #else:
52e5c0f2907f Uploaded bgruening parents: diff changeset	45 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
52e5c0f2907f Uploaded bgruening parents: diff changeset	46 ## 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.
52e5c0f2907f Uploaded bgruening parents: diff changeset	47 ## A workaround is to create a symlink with a proper file-extension.
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	48 ln -s '$method_opts.query' ./temp_query.$method_opts.query.ext
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	49 obabel
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	50 -i fs '$method_opts.fastsearch.files_path/molecule.fs'
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	51 -S ./temp_query.$method_opts.query.ext
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	52 -at${method_opts.threshold}
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	53 -O '${outfile}'
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	54 -osmi
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	55 -aa
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	56 #end if
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	57 ]]>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	58 </command>
52e5c0f2907f Uploaded bgruening parents: diff changeset	59 <inputs>
52e5c0f2907f Uploaded bgruening parents: diff changeset	60 <conditional name="method_opts">
52e5c0f2907f Uploaded bgruening parents: diff changeset	61 <param name="method_opts_selector" type="select" label="Subject database/sequences">
52e5c0f2907f Uploaded bgruening parents: diff changeset	62 <option value="chemfp">Chemfp fingerprint file</option>
52e5c0f2907f Uploaded bgruening parents: diff changeset	63 <option value="obabel">OpenBabel Fastsearch Index</option>
52e5c0f2907f Uploaded bgruening parents: diff changeset	64 </param>
52e5c0f2907f Uploaded bgruening parents: diff changeset	65 <when value="chemfp">
52e5c0f2907f Uploaded bgruening parents: diff changeset	66 <conditional name="query_opts">
2 497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	67 <param name="query_opts_selector" type="select" label="Query mode">
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	68 <option value="normal">Query molecules are stores in a separate file</option>
52e5c0f2907f Uploaded bgruening parents: diff changeset	69 <option value="nxn">Target molecules are also queries (NxN)</option>
52e5c0f2907f Uploaded bgruening parents: diff changeset	70 </param>
52e5c0f2907f Uploaded bgruening parents: diff changeset	71 <when value="normal">
52e5c0f2907f Uploaded bgruening parents: diff changeset	72 <param name='query' type='data' format="fps" label='Query molecules'/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	73 <param name='targets' type='data' format="fps" label='Target molecules'/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	74 </when>
52e5c0f2907f Uploaded bgruening parents: diff changeset	75 <when value="nxn">
52e5c0f2907f Uploaded bgruening parents: diff changeset	76 <param name='targets' type='data' format="fps" label='Target moleculs'/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	77 </when>
52e5c0f2907f Uploaded bgruening parents: diff changeset	78 </conditional>
2 497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	79 <param name='knn' type='integer' value='0' label='Select the k nearest neighbors' help='0 means all neighbors'>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	80 <validator type="in_range" min="0" />
52e5c0f2907f Uploaded bgruening parents: diff changeset	81 </param>
2 497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	82 <param name='threshold' type='float' value='0.7' label='Minimum similarity score threshold' />
497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	83 <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 52e5c0f2907f Uploaded bgruening parents: diff changeset	84 </when>
52e5c0f2907f Uploaded bgruening parents: diff changeset	85 <when value="obabel">
2 497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	86 <param name="query" type='data' format="smi,mol,sdf,inchi" label="Query"/>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	87 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
2 497254c6c09e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit ed9b6859de648aa5f7cde483732f5df20aaff90e bgruening parents: 1 diff changeset	88 <param name="threshold" type='float' label="Minimum similarity score threshold" value='0.7'/>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	89 </when>
52e5c0f2907f Uploaded bgruening parents: diff changeset	90 </conditional>
52e5c0f2907f Uploaded bgruening parents: diff changeset	91
52e5c0f2907f Uploaded bgruening parents: diff changeset	92 </inputs>
52e5c0f2907f Uploaded bgruening parents: diff changeset	93 <outputs>
52e5c0f2907f Uploaded bgruening parents: diff changeset	94 <data name="outfile" format="tabular" />
52e5c0f2907f Uploaded bgruening parents: diff changeset	95 </outputs>
52e5c0f2907f Uploaded bgruening parents: diff changeset	96 <tests>
52e5c0f2907f Uploaded bgruening parents: diff changeset	97 <test>
52e5c0f2907f Uploaded bgruening parents: diff changeset	98 <param name="targets" ftype="fps" value="targets.fps"/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	99 <param name="query" ftype="fps" value="q.fps"/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	100 <param name="k" value='4'/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	101 <param name="th" value='0.7'/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	102 <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
52e5c0f2907f Uploaded bgruening parents: diff changeset	103 </test>
52e5c0f2907f Uploaded bgruening parents: diff changeset	104 </tests>
52e5c0f2907f Uploaded bgruening parents: diff changeset	105 <help>
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	106 <![CDATA[
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	107
52e5c0f2907f Uploaded bgruening parents: diff changeset	108
52e5c0f2907f Uploaded bgruening parents: diff changeset	109 .. class:: infomark
52e5c0f2907f Uploaded bgruening parents: diff changeset	110
52e5c0f2907f Uploaded bgruening parents: diff changeset	111 What this tool does
52e5c0f2907f Uploaded bgruening parents: diff changeset	112
52e5c0f2907f Uploaded bgruening parents: diff changeset	113 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
52e5c0f2907f Uploaded bgruening parents: diff changeset	114
52e5c0f2907f Uploaded bgruening parents: diff changeset	115 .. _chemfp: http://chemfp.com/
52e5c0f2907f Uploaded bgruening parents: diff changeset	116 .. _FastSearch: http://openbabel.org/wiki/FastSearch
52e5c0f2907f Uploaded bgruening parents: diff changeset	117
52e5c0f2907f Uploaded bgruening parents: diff changeset	118
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	119 ]]>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	120 </help>
1 0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	121 <citations>
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	122 <citation type="doi">10.1186/1758-2946-3-33</citation>
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	123 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
0892f7ced10c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit d786052cd04f8b25eb4aff80b1b9724f62031b61 bgruening parents: 0 diff changeset	124 </citations>
0 52e5c0f2907f Uploaded bgruening parents: diff changeset	125 </tool>

Mercurial > repos > bgruening > simsearch

annotate simsearch.xml @ 3:9f1a8df0b437 draft