Mercurial > repos > bgruening > rxdock_rbdock
comparison rbdock.xml @ 0:35ee2e002bb0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
author | bgruening |
---|---|
date | Sat, 04 Apr 2020 15:00:22 -0400 |
parents | |
children | 07309bad01df |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:35ee2e002bb0 |
---|---|
1 <tool id="rxdock_rbdock" name="rxDock docking" version="0.1.3" profile="19.01"> | |
2 <description>- perform protein-ligand docking with rxDock</description> | |
3 <macros> | |
4 <import>rdock_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command><![CDATA[ | |
8 ln -s '$active_site' receptor.as && | |
9 ln -s '$receptor' receptor.mol2 && | |
10 ln -s $receptor_prm receptor.prm && | |
11 #if $name == 'Y': | |
12 sdmodify -f_REC '$ligands' > ligands.sdf && | |
13 #else | |
14 ln -s '$ligands' ligands.sdf && | |
15 #end if | |
16 | |
17 python '$__tool_directory__/rbdock.py' | |
18 -n '$num' | |
19 #if $seed: | |
20 -s '$seed' | |
21 #end if | |
22 && | |
23 | |
24 cat rdock_output.sd | |
25 | |
26 #if $filter.filter_select == "filter": | |
27 #if $filter.score: | |
28 | sdfilter -f'\$SCORE <= ${filter.score}' | |
29 #end if | |
30 #if $filter.nscore: | |
31 | sdfilter -f'\$SCORE.norm <= ${filter.nscore}' | |
32 #end if | |
33 #if $filter.top | |
34 | sdsort -n -s -fSCORE | sdfilter -f'\$_COUNT <= $filter.top' | |
35 #end if | |
36 #end if | |
37 | |
38 > '$output' | |
39 | |
40 ]]></command> | |
41 | |
42 <configfiles> | |
43 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00 | |
44 RECEPTOR_FILE receptor.mol2 | |
45 RECEPTOR_FLEX 3.0 | |
46 </configfile> | |
47 </configfiles> | |
48 | |
49 <inputs> | |
50 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/> | |
51 <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/> | |
52 <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/> | |
53 <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/> | |
54 <conditional name="filter"> | |
55 <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter"> | |
56 <option value="filter">Show filter options</option> | |
57 <option value="no_filter">No filtering</option> | |
58 </param> | |
59 <when value="filter"> | |
60 <param name="score" type="float" optional="true" label="Score filter" | |
61 help="Exclude poses with score greater than this value"/> | |
62 <param name="nscore" type="float" optional="true" label="Normalised score filter" | |
63 help="Exclude poses with normalised score greater than this value"/> | |
64 <param name="top" type="integer" value="1" optional="true" min="1" label="Number of best poses" | |
65 help="Number of best scoring poses to keep"/> | |
66 </when> | |
67 <when value="no_filter"/> | |
68 </conditional> | |
69 <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false" | |
70 help="Generate the name field (first line) for cases where this is empty"/> | |
71 <param argument="-seed" type="integer" optional="true" label="Random seed" help=""/> | |
72 </inputs> | |
73 <outputs> | |
74 <data name="output" format="sdf" label="rxDock on ${on_string}"/> | |
75 </outputs> | |
76 <tests> | |
77 <!-- broken ligand test --> | |
78 <test expect_failure="true" expect_exit_code="23"> | |
79 <param name="receptor" value="receptor.mol2"/> | |
80 <param name="ligands" value="broken_ligand.sdf"/> | |
81 <param name="active_site" value="receptor.as"/> | |
82 <param name="num" value="3"/> | |
83 <param name="seed" value="3"/> | |
84 <conditional name="filter"> | |
85 <param name="filter_select" value="filter"/> | |
86 <param name="top" value="1"/> | |
87 </conditional> | |
88 <param name="name" value="false"/> | |
89 </test> | |
90 <test> | |
91 <param name="receptor" value="receptor.mol2"/> | |
92 <param name="ligands" value="ligands_names.sdf"/> | |
93 <param name="active_site" value="receptor.as"/> | |
94 <param name="num" value="3"/> | |
95 <param name="seed" value="3"/> | |
96 <conditional name="filter"> | |
97 <param name="filter_select" value="filter"/> | |
98 <param name="top" value="1"/> | |
99 </conditional> | |
100 <param name="name" value="false"/> | |
101 <output name="output"> | |
102 <assert_contents> | |
103 <has_text text="Rbt.Current_Directory"/> | |
104 <has_n_lines n="355"/> | |
105 </assert_contents> | |
106 </output> | |
107 </test> | |
108 <test> | |
109 <param name="receptor" value="receptor.mol2"/> | |
110 <param name="ligands" value="ligands_nonames.sdf"/> | |
111 <param name="active_site" value="receptor.as"/> | |
112 <param name="num" value="3"/> | |
113 <param name="seed" value="3"/> | |
114 <conditional name="filter"> | |
115 <param name="filter_select" value="filter"/> | |
116 <param name="top" value="1"/> | |
117 </conditional> | |
118 <param name="name" value="true"/> | |
119 <output name="output"> | |
120 <assert_contents> | |
121 <has_text text="Rbt.Current_Directory"/> | |
122 <has_n_lines n="355"/> | |
123 </assert_contents> | |
124 </output> | |
125 </test> | |
126 <!-- no filter test --> | |
127 <test> | |
128 <param name="receptor" value="receptor.mol2"/> | |
129 <param name="ligands" value="ligands_nonames.sdf"/> | |
130 <param name="active_site" value="receptor.as"/> | |
131 <param name="num" value="3"/> | |
132 <param name="seed" value="3"/> | |
133 <conditional name="filter"> | |
134 <param name="filter_select" value="no_filter"/> | |
135 </conditional> | |
136 <param name="name" value="true"/> | |
137 <output name="output"> | |
138 <assert_contents> | |
139 <has_text text="Rbt.Current_Directory"/> | |
140 <has_n_lines n="1059"/> | |
141 </assert_contents> | |
142 </output> | |
143 </test> | |
144 <test> | |
145 <param name="receptor" value="receptor.mol2"/> | |
146 <param name="ligands" value="ligands_names.sdf"/> | |
147 <param name="active_site" value="receptor.as"/> | |
148 <param name="num" value="1"/> | |
149 <param name="seed" value="3"/> | |
150 <conditional name="filter"> | |
151 <param name="filter_select" value="filter"/> | |
152 <param name="score" value="10"/> | |
153 <param name="nscore" value="1"/> | |
154 </conditional> | |
155 <param name="name"/> | |
156 <output name="output"> | |
157 <assert_contents> | |
158 <has_text text="Rbt.Current_Directory"/> | |
159 <has_n_lines n="355"/> | |
160 </assert_contents> | |
161 </output> | |
162 </test> | |
163 </tests> | |
164 <help><![CDATA[ | |
165 | |
166 .. class:: infomark | |
167 | |
168 This tool performs protein-ligand docking using the rxDock program. | |
169 See https://www.rxdock.org for more details about rxDock and associated programs. | |
170 | |
171 ----- | |
172 | |
173 .. class:: infomark | |
174 | |
175 **Inputs** | |
176 | |
177 1. The protein receptor to dock into as a file in Mol2 format. | |
178 2. The active site definition as a file as generated by the rbcavity tool. | |
179 3. A set of ligands (collection or single file) to dock as a file in SDF format. | |
180 4. The number of docking poses to generate (integer). | |
181 5. The number of best scoring dockings to keep (integer). | |
182 6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional). | |
183 7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed. | |
184 Poses with normalised scores greater than this are excluded (float, optional). | |
185 8. Optionally generate the name field in the ligands SDF (this is the first line in the entry). | |
186 This field must be present and be unique for sorting and filtering to work. If your results contain only one record | |
187 then the name field is probably absent and must be generated. | |
188 | |
189 You will need to perform some test dockings to establish suitable values for the score filters. | |
190 The score is a number with lower values being better. Values can be negative. | |
191 | |
192 ----- | |
193 | |
194 .. class:: infomark | |
195 | |
196 **Outputs** | |
197 | |
198 An SDF file is produced as output. The binding affinity scores are contained within the SDF file.:: | |
199 | |
200 1-pyrimethamine | |
201 rDOCK(R) 3D | |
202 libRbt.so/2013.1/901 2013/11/27 | |
203 21 22 0 0 0 0 0 0 0 0999 V2000 | |
204 -5.1897 17.8912 17.9590 N 0 0 0 0 0 0 | |
205 -3.9121 17.9973 18.3210 C 0 0 0 0 0 0 | |
206 -3.2404 19.1465 18.3804 N 0 0 0 0 0 0 | |
207 -3.8989 20.2829 18.0453 C 0 0 0 0 0 0 | |
208 -5.2389 20.2802 17.6553 C 0 0 0 0 0 0 | |
209 -5.8448 19.0235 17.6464 C 0 0 0 0 0 0 | |
210 -5.9601 21.5065 17.2850 C 0 0 0 0 0 0 | |
211 -6.2108 22.5074 18.2382 C 0 0 0 0 0 0 | |
212 -6.8903 23.6771 17.8851 C 0 0 0 0 0 0 | |
213 -7.3267 23.8556 16.5746 C 0 0 0 0 0 0 | |
214 -7.0903 22.8744 15.6151 C 0 0 0 0 0 0 | |
215 -6.4107 21.7051 15.9695 C 0 0 0 0 0 0 | |
216 -3.2455 16.8582 18.6507 N 0 0 0 0 0 0 | |
217 -7.1550 18.8446 17.2393 N 0 0 0 0 0 0 | |
218 -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0 | |
219 -2.9891 22.1828 19.5033 C 0 0 0 0 0 0 | |
220 -3.1112 21.5771 18.1096 C 0 0 0 0 0 0 | |
221 -2.2766 16.9101 18.9273 H 0 0 0 0 0 0 | |
222 -3.7237 15.9703 18.6154 H 0 0 0 0 0 0 | |
223 -7.8809 19.3992 17.6807 H 0 0 0 0 0 0 | |
224 -7.4159 17.8951 16.9940 H 0 0 0 0 0 0 | |
225 1 2 2 0 0 0 | |
226 1 6 1 0 0 0 | |
227 2 3 1 0 0 0 | |
228 2 13 1 0 0 0 | |
229 3 4 2 0 0 0 | |
230 4 5 1 0 0 0 | |
231 4 17 1 0 0 0 | |
232 5 6 2 0 0 0 | |
233 5 7 1 0 0 0 | |
234 6 14 1 0 0 0 | |
235 7 8 2 0 0 0 | |
236 7 12 1 0 0 0 | |
237 8 9 1 0 0 0 | |
238 9 10 2 0 0 0 | |
239 10 11 1 0 0 0 | |
240 10 15 1 0 0 0 | |
241 11 12 2 0 0 0 | |
242 13 18 1 0 0 0 | |
243 13 19 1 0 0 0 | |
244 14 20 1 0 0 0 | |
245 14 21 1 0 0 0 | |
246 16 17 1 0 0 0 | |
247 M END | |
248 > <CHROM.0> | |
249 -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150 | |
250 | |
251 > <CHROM.1> | |
252 -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835 | |
253 0.96119776,0.49809360,-3.12917831 | |
254 | |
255 > <Rbt.Current_Directory> | |
256 /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock | |
257 | |
258 > <Rbt.Executable> | |
259 rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) | |
260 | |
261 > <Rbt.Library> | |
262 libRbt.so (2013.1, Build901 2013/11/27) | |
263 | |
264 > <Rbt.Parameter_File> | |
265 /rDock_2013.1/data/scripts/dock.prm | |
266 | |
267 > <Rbt.Receptor> | |
268 receptor.prm | |
269 | |
270 > <SCORE> | |
271 0.445364 | |
272 | |
273 > <SCORE.INTER> | |
274 8.4 | |
275 | |
276 > <SCORE.INTER.CONST> | |
277 1 | |
278 | |
279 > <SCORE.INTER.POLAR> | |
280 0 | |
281 | |
282 > <SCORE.INTER.REPUL> | |
283 0 | |
284 | |
285 > <SCORE.INTER.ROT> | |
286 3 | |
287 | |
288 > <SCORE.INTER.VDW> | |
289 0 | |
290 | |
291 > <SCORE.INTER.norm> | |
292 0.494118 | |
293 | |
294 > <SCORE.INTRA> | |
295 -1.38672 | |
296 | |
297 > <SCORE.INTRA.DIHEDRAL> | |
298 -0.818539 | |
299 | |
300 > <SCORE.INTRA.DIHEDRAL.0> | |
301 6.01924 | |
302 | |
303 > <SCORE.INTRA.POLAR> | |
304 0 | |
305 | |
306 > <SCORE.INTRA.POLAR.0> | |
307 0 | |
308 | |
309 > <SCORE.INTRA.REPUL> | |
310 0 | |
311 | |
312 > <SCORE.INTRA.REPUL.0> | |
313 0 | |
314 | |
315 > <SCORE.INTRA.VDW> | |
316 -0.977448 | |
317 | |
318 > <SCORE.INTRA.VDW.0> | |
319 -1.0079 | |
320 | |
321 > <SCORE.INTRA.norm> | |
322 -0.0815716 | |
323 | |
324 > <SCORE.RESTR> | |
325 | |
326 > <SCORE.RESTR.norm> | |
327 0 | |
328 | |
329 > <SCORE.SYSTEM> | |
330 -6.56792 | |
331 | |
332 > <SCORE.SYSTEM.CONST> | |
333 0 | |
334 | |
335 > <SCORE.SYSTEM.DIHEDRAL> | |
336 1.50415 | |
337 | |
338 > <SCORE.SYSTEM.POLAR> | |
339 -2.3289 | |
340 | |
341 > <SCORE.SYSTEM.VDW> | |
342 0.59827 | |
343 | |
344 > <SCORE.SYSTEM.norm> | |
345 -0.386348 | |
346 | |
347 > <SCORE.heavy> | |
348 17 | |
349 | |
350 > <SCORE.norm> | |
351 0.0261979 | |
352 | |
353 $$$$ | |
354 | |
355 ]]></help> | |
356 <expand macro="citations"/> | |
357 </tool> |