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comparison acpc.xml @ 3:8c2e85bb2ce9 draft

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planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
author marpiech
date Tue, 20 Sep 2016 09:57:24 -0400
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2:958fa7ba4715 3:8c2e85bb2ce9
1 <tool id="acpc" name="ACPC" version="1.0">
2 <description>Chemoinformatics tool for ligand-based virtual screening</description>
3 <stdio>
4 <exit_code range="1:" />
5 </stdio>
6 <command>
7 <![CDATA[
8 #if $program_chose.program=="acpc" #
9 if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then
10 cat $program_chose.q > query.mol2;
11 cat $program_chose.db > database.mol2 ;
12 else
13 if cat $program_chose.q | grep "BEGIN" > /dev/null; then
14 cat $program_chose.q > query.pl;
15 cat $program_chose.db > database.pl ;
16 else
17 cat $program_chose.q > query.pqr;
18 cat $program_chose.db > database.pqr ;
19 fi;
20 fi;
21 acpc
22 -q query.*
23 -db database.*
24 #if $program_chose.top_mol.top_scoring_mol=="true"
25 -top $program_chose.top_mol.top
26 -o mol_output
27 #end if
28 #if $program_chose.a
29 -a $program_chose.a
30 #end if
31 #if $program_chose.nopp=="true"
32 -nopp
33 #end if
34 #if $program_chose.er
35 -er $program_chose.er
36 #end if
37 #if $program_chose.scan=="true"
38 -scan scan_out
39 #end if
40 -v
41 ;
42 cat *.scores > $score_output_acpc;
43 #if $program_chose.top_mol.top_scoring_mol=="true" #
44 cat mol_output > $mol_output_acpc;
45 #end if #
46 #if $program_chose.scan=="true" #
47 cat scan_out > $scan_output_acpc;
48 cat query.mol2.bld > $bld_output_acpc;
49 #end if #
50 #end if #
51 #if $program_chose.program=="acpc_mol2tool" #
52 cat $program_chose.i > query.mol2;
53 acpc_mol2tool -i query.mol2;
54 mkdir results;
55 mv query_*/* results/. ;
56 #end if #
57 #if $program_chose.program=="acpc_par" #
58 if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then
59 cat $program_chose.q > query.mol2;
60 cat $program_chose.db > database.mol2 ;
61 else
62 if cat $program_chose.q | grep "BEGIN" > /dev/null; then
63 cat $program_chose.q > query.pl;
64 cat $program_chose.db > database.pl ;
65 else
66 cat $program_chose.q > query.pqr;
67 cat $program_chose.db > database.pqr ;
68 fi;
69 fi;
70 acpc_par
71 -q query.*
72 -db database.*
73 -o score
74 #if $program_chose.a
75 -a $a
76 #end if
77 #if $program_chose.np
78 -np $np
79 #end if
80 ;
81 cat score > $output_acpc_par;
82 #end if #
83 #if $program_chose.program=="acpc_pqrtool" #
84 cat $program_chose.pqrfile > pqrfile.pqr;
85 acpc_pqrtool pqrfile.pqr > $output_acpc_pqrtool;
86 #end if #
87 #if $program_chose.program=="acpc_mol2reader" #
88 cat $program_chose.mol2file > mol2file.mol2;
89 acpc_mol2reader mol2file.mol2 > $output_acpc_mol2reader;
90 #end if #
91 #if $program_chose.program=="acpc_auctool" #
92 cat $program_chose.i > score.scores;
93 acpc_auctool -i score.scores -p $program_chose.p > $output_acpc_auctool;
94 #end if #
95 #if $program_chose.program=="acpc_pltool" #
96 cat $program_chose.plfile > plfile.pl;
97 acpc_pltool plfile.pl > $output_acpc_pltool;
98 #end if #
99
100 ]]>
101 </command>
102 <inputs>
103 <conditional name="program_chose">
104 <param name="program" type="select" label="Chose a program ">
105 <option value="acpc" selected="true">acpc </option>
106 <!-- <option value="acpc_consrank">acpc_consrank </option> -->
107 <option value="acpc_mol2tool">acpc_mol2tool </option>
108 <option value="acpc_pqrtool">acpc_pqrtool </option>
109 <option value="acpc_auctool">acpc_auctool </option>
110 <!-- <option value="acpc_ertool">acpc_ertool </option> -->
111 <option value="acpc_par">acpc_par </option>
112 <!-- <option value="acpc_scorer">acpc_scorer </option> -->
113 <!-- <option value="acpc_codec">acpc_codec </option> -->
114 <option value="acpc_mol2reader">acpc_mol2reader </option>
115 <option value="acpc_pltool">acpc_pltool </option>
116 </param>
117 <when value="acpc">
118 <param name="q" type="data" format="mol2,pqr,pl" label="Query" help="acpc (-q)" />
119 <param name="db" type="data" format="mol2,pqr,pl" label="Database" help="acpc (-db)" />
120 <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc (-a)" optional="true" />
121 <param name="er" type="float" label="Enrichment rate parameter; e.g. 0.01 --> ER_1%" help="acpc (-er)" optional="true">
122 <validator type="in_range" min="0" max="1" />
123 </param>
124 <param name="nopp" type="select" label="Don't rm duplicate molecules (based on names)" help="acpc (-nopp)">
125 <option value="false" selected="true">Don't use this option</option>
126 <option value="true">Use this option</option>
127 </param>
128 <param name="scan" type="select" label="Scan delta AUC per atom in the query and create a new query molecule" help="acpc (-scan)">
129 <option value="false" selected="true">Don't use this option</option>
130 <option value="true">Use this option</option>
131 </param>
132 <conditional name="top_mol" >
133 <param name="top_scoring_mol" type="select" label="Return file with top scoring molecules (only works for MOL2 files)" >
134 <option value="false" selected="true">Don't use this option</option>
135 <option value="true">Use this option</option>
136 </param>
137 <when value="false" >
138 </when>
139 <when value="true" >
140 <param name="top" type="integer" value="1" label="Number of top scoring molecules to output" help="acpc (-top)" />
141 </when>
142 </conditional>
143 </when>
144 <!-- <when value="acpc_consrank"> -->
145 <!-- </when> -->
146 <when value="acpc_mol2tool">
147 <param name="i" type="data" format="mol2" label="Input mol2 file" help="acpc_mol2tool (-i)" />
148 </when>
149 <when value="acpc_pqrtool">
150 <param name="pqrfile" type="data" format="pqr" label="Input pqr file" />
151 </when>
152 <when value="acpc_auctool">
153 <param name="i" type="data" format="data" label="Input score file" />
154 <param name="p" type="text" value="0.05" label="A float such that x in (0.0; 1.0] " />
155 </when>
156 <!-- <when value="acpc_ertool"> -->
157 <!-- </when> -->
158 <when value="acpc_par">
159 <param name="q" type="data" format="mol2" label="Query" help="acpc_par (-q)" />
160 <param name="db" type="data" format="mol2" label="Database" help="acpc_par (-db)" />
161 <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc_par (-a)" optional="true" />
162 <param name="np" type="integer" label="Max number of cores to use" help="acpc_par (-np)" optional="true" />
163 </when>
164 <!-- <when value="acpc_scorer"> -->
165 <!-- </when> -->
166 <!-- <when value="acpc_codec"> -->
167 <!-- </when> -->
168 <when value="acpc_mol2reader">
169 <param name="mol2file" type="data" format="mol2" label="Input mol2 file" />
170 </when>
171 <when value="acpc_pltool">
172 <param name="plfile" type="data" format="pl" label="Input pl file" />
173 </when>
174 </conditional>
175 </inputs>
176 <outputs>
177 <data name="mol_output_acpc" format="txt" label="ACPC: output molecules" >
178 <filter>program_chose["program"]=="acpc" and program_chose["top_mol"]["top_scoring_mol"]=="true"</filter>
179 </data>
180 <data name="score_output_acpc" format="txt" label="ACPC: score" >
181 <filter>program_chose["program"]=="acpc"</filter>
182 </data>
183 <data name="scan_output_acpc" format="txt" label="ACPC: scan file">
184 <filter>program_chose["program"]=="acpc" and program_chose["scan"]=="true"</filter>
185 </data>
186 <data name="bld_output_acpc" format="txt" label="ACPC: mol2.bld file">
187 <filter>program_chose["program"]=="acpc"</filter>
188 <filter>program_chose["scan"]=="true"</filter>
189 </data>
190 <data format="txt" name="report">
191 <filter>program_chose["program"]=="acpc_mol2tool"</filter>
192 <discover_datasets pattern="([0123456789]*)\.mol2" directory="results" visible="true" />
193 </data>
194 <data name="output_acpc_par" format="txt" label="ACPC: score file">
195 <filter>program_chose["program"]=="acpc_par" </filter>
196 </data>
197 <data name="output_acpc_mol2reader" format="txt" label="ACPC mol2reader output">
198 <filter>program_chose["program"]=="acpc_mol2reader" </filter>
199 </data>
200 <data name="output_acpc_pltool" format="txt" label="ACPC pltool output">
201 <filter>program_chose["program"]=="acpc_pltool" </filter>
202 </data>
203 <data name="output_acpc_auctool" format="txt" label="ACPC auctool output">
204 <filter>program_chose["program"]=="acpc_auctool" </filter>
205 </data>
206 <data name="output_acpc_pqrtool" format="txt" label="ACPC pqrtool output">
207 <filter>program_chose["program"]=="acpc_pqrtool" </filter>
208 </data>
209 </outputs>
210 <tests>
211 <test>
212 <param name="program" value="acpc" />
213 <param name="top_scoring_mol" value="true" />
214 <param name="q" value="acpc/query.mol2" />
215 <param name="db" value="acpc/database.mol2" />
216 <output name="mol_output_acpc" file="acpc/output"/>
217 </test>
218 <test>
219 <param name="program" value="acpc_mol2reader" />
220 <param name="mol2file" value="acpc/query.mol2" />
221 <output name="output_acpc_mol2reader" file="acpc/output_mol2reader"/>
222 </test>
223 </tests>
224 <help>
225 <![CDATA[
226 ************
227 Description
228 ************
229 ACPC is a ligand-based virtual screening tool using AutoCorrelation of Partial Charges.
230
231 *******
232 Help
233 *******
234
235 acpc
236
237 --a float kernel parameter (default depends on considered feature space and was optimized on DUD-E)
238 --db db database in .mol2, .pl or .pqr format
239 --er x enrichment rate parameter; e.g. 0.01 --> ER_1%
240 --nopp don't rm duplicate molecules (based on names)
241 --q query query in .mol2, .pl or .pqr format
242 --scan out_file scan delta AUC per atom in the query and create a new query molecule
243 --top int number of top scoring molecules to output (only works for MOL2 files)
244
245
246 acpc_mol2tool
247
248 --i in input mol2 file
249
250 acpc_auctool
251
252 -i in input scores file
253 -p x a float such that 0.0 < x <= 1.0
254
255
256
257 acpc_par
258
259 --a float kernel parameter (default was optimized on DUD-E and depends on considered feature space)
260 --db db molecules database in .mol2, .pl or .pqr format
261 --q query molecule in .mol2, .pl or .pqr format
262 --np int max number of cores to use
263
264 ]]>
265 </help>
266 <citations>
267 <citation type="bibtex">
268 @article{Berenger2014,
269 doi = {10.1186/1758-2946-6-23},
270 url = {http://dx.doi.org/10.1186/1758-2946-6-23},
271 year = {2014},
272 publisher = {Springer Nature},
273 volume = {6},
274 number = {1},
275 pages = {23},
276 author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
277 title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
278 journal = {Journal of Cheminformatics}
279 }
280 </citation>
281 </citations>
282 </tool>