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comparison mol2fps.xml @ 2:70b071de9bee draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:31:44 -0400
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1:43a9e7d9b24f 2:70b071de9bee
1 <tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0">
2 <description>with different fingerprint types</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
4 <requirements>
5 <requirement type="package" version="1.1p1">chemfp</requirement>
6 <requirement type="package" version="2016.03.3">rdkit</requirement>
7 <requirement type="package" version="2.4.1">openbabel</requirement>
8 </requirements>
9 <command>
10 <![CDATA[
11 #set $fptype = $fp_opts.fp_opts_selector
12
13 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
14 ## Open Babel fingerprints
15 ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}'
16 #else:
17 ## RDKit fingerprints
18 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}'
19 #if $fp_opts.fp_opts_selector == "--RDK":
20 --RDK
21 --fpSize $fp_opts.fpSize
22 --minPath $fp_opts.minPath
23 --maxPath $fp_opts.maxPath
24 --nBitsPerHash $fp_opts.nBitsPerHash
25 $fp_opts.useHs
26 #elif $fp_opts.fp_opts_selector == "--torsions":
27 --torsions
28 --fpSize $fp_opts.fpSize
29 --targetSize $fp_opts.targetSize
30 #elif $fp_opts.fp_opts_selector == "--morgan":
31 --morgan
32 --fpSize $fp_opts.fpSize
33 --radius $fp_opts.radius
34 $fp_opts.useFeatures
35 $fp_opts.useChirality
36 $fp_opts.useBondTypes
37 #elif $fp_opts.fp_opts_selector == "--pairs":
38 --paris
39 --fpSize $fp_opts.fpSize
40 --minLength $fp_opts.minLength
41 --maxLength $fp_opts.maxLength
42 #elif $fp_opts.fp_opts_selector == "--maccs166":
43 --maccs166
44 #elif $fp_opts.fp_opts_selector == "--substruct":
45 --substruct
46 #end if
47 #end if
48 --errors report 2>&1
49 ]]>
50 </command>
51 <inputs>
52 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
53 <conditional name="fp_opts">
54 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
55 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
56 <option value='--FP3'>Open Babel FP3 fingerprints</option>
57 <option value='--FP4'>Open Babel FP4 fingerprints</option>
58 <option value='--MACCS'>Open Babel MACCS fingerprints</option>
59 <option value='--RDK'>RDKit topological fingerprint</option>
60 <option value='--torsions'>RDKit topological Torsion fingerprints</option>
61 <option value='--morgan'>RDKit Morgan fingerprints</option>
62 <option value='--pairs'>RDKit Atom Pair fingerprints</option>
63 <option value='--maccs166'>RDKit MACCS fingerprints</option>
64 <option value='--substruct'>RDKit substructure fingerprints</option>
65 </param>
66 <when value="--FP2" />
67 <when value="--FP3" />
68 <when value="--FP4" />
69 <when value="--MACCS" />
70 <when value="--RDK">
71 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
72 <validator type="in_range" min="1" />
73 </param>
74 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
75 <validator type="in_range" min="1" />
76 </param>
77 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
78 <validator type="in_range" min="1" />
79 </param>
80 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
81 <validator type="in_range" min="1" />
82 </param>
83 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true"
84 label="include information about the number of hydrogens on each atom" />
85 </when>
86 <when value="--torsions">
87 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
88 <validator type="in_range" min="1" />
89 </param>
90 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
91 <validator type="in_range" min="1" />
92 </param>
93 </when>
94 <when value="--morgan">
95 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
96 <validator type="in_range" min="1" />
97 </param>
98 <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
99 <validator type="in_range" min="1" />
100 </param>
101 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false"
102 label="include information about the number of hydrogens on each atom" />
103 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false"
104 label="include information about the number of hydrogens on each atom" />
105 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true"
106 label="include information about the number of hydrogens on each atom" />
107 </when>
108 <when value="--pairs">
109 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
110 <validator type="in_range" min="1" />
111 </param>
112 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
113 <validator type="in_range" min="1" />
114 </param>
115 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
116 <validator type="in_range" min="1" />
117 </param>
118 </when>
119 <when value="--maccs166" />
120 <when value="--substruct" />
121 </conditional>
122
123 </inputs>
124 <outputs>
125 <data name="outfile" format="fps" />
126 </outputs>
127 <tests>
128 <!-- FP2 -->
129 <test>
130 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
131 <param name="fp_opts.fp_opts_selector" value="--FP2" />
132 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
133 </test>
134 <test>
135 <param name="infile" value="CID_2244.smi" ftype="smi" />
136 <param name="fp_opts.fp_opts_selector" value="--FP2" />
137 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
138 </test>
139 <!-- FP3 -->
140 <test>
141 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
142 <param name="fp_opts.fp_opts_selector" value="--FP3" />
143 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
144 </test>
145 <test>
146 <param name="infile" value="CID_2244.smi" ftype="smi" />
147 <param name="fp_opts.fp_opts_selector" value="--FP3" />
148 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
149 </test>
150 <!-- FP4 -->
151 <test>
152 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
153 <param name="fp_opts.fp_opts_selector" value="--FP4" />
154 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
155 </test>
156 <test>
157 <param name="infile" value="CID_2244.smi" ftype="smi" />
158 <param name="fp_opts.fp_opts_selector" value="--FP4" />
159 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
160 </test>
161 <!-- MACCS -->
162 <test>
163 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
164 <param name="fp_opts.fp_opts_selector" value="--MACCS" />
165 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
166 </test>
167 <test>
168 <param name="infile" value="CID_2244.smi" ftype="smi" />
169 <param name="fp_opts.fp_opts_selector" value="--MACCS" />
170 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
171 </test>
172 </tests>
173 <help>
174 <![CDATA[
175
176 .. class:: infomark
177
178 **What this tool does**
179
180 This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_.
181
182 For more information check the websites listed below::
183
184 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
185 - http://openbabel.org/wiki/Tutorial:Fingerprints
186
187 -----
188
189 .. class:: infomark
190
191 **Input**
192
193 FPS fingerprint file format
194
195 * Example::
196
197 - SDF File
198
199 28434379
200 -OEChem-02031205132D
201
202 37 39 0 0 0 0 0 0 0999 V2000
203 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
204 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
205 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
206 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
207 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
208 7.3704 0.9433 0.0000 C 0 0 0 0
209 ......
210 1 15 1 0 0 0 0
211 1 35 1 0 0 0 0
212 2 5 1 0 0 0 0
213 2 11 1 0 0 0 0
214 2 12 1 0 0 0 0
215 3 12 2 0 0 0 0
216 3 13 1 0 0 0 0
217 4 18 1 0 0 0 0
218 ......
219
220 >PUBCHEM_COMPOUND_CID<
221 28434379
222
223 > <PUBCHEM_COMPOUND_CANONICALIZED>
224 1
225
226 > <PUBCHEM_CACTVS_COMPLEXITY>
227 280
228
229 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
230 2
231
232 > <PUBCHEM_CACTVS_HBOND_DONOR>
233 2
234
235 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
236 2
237
238 > <PUBCHEM_CACTVS_SUBSKEYS>
239 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
240
241 >
242
243 - type : FP2
244
245 -----
246
247 .. class:: infomark
248
249 **Output**
250
251 * Example::
252
253 #FPS1
254 #num_bits=1021
255 #type=OpenBabel-FP2/1
256 #software=OpenBabel/2.3.0
257 #source=/tmp/dataset_409.dat.sdf
258 #date=2012-02-03T11:13:39
259 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
260 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
261 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
262
263
264 ]]>
265 </help>
266 <citations>
267 <citation type="doi">10.1186/1758-2946-3-33</citation>
268 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
269 <citation type="bibtex">
270 @electronic{rdkit,
271 title = {RDKit: Open-source cheminformatics},
272 url ={http://www.rdkit.org}
273 }
274 </citation>
275 </citations>
276 </tool>