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comparison parmconv.xml @ 3:2b82fc7bec67 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit cc13bd32ef2d80b01dc197a3ca120a4ff9f0dacc"
author chemteam
date Fri, 12 Mar 2021 12:32:24 +0000
parents da2252f1ccab
children 267a70416daf
comparison
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2:b500cc25dd15 3:2b82fc7bec67
1 <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>to AMBER prmtop in preparation for MMPBSA</description> 2 <description>to AMBER prmtop in preparation for MMGBSA/MMPBSA</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="3.2.0">parmed</requirement> 8 <requirement type="package" version="3.2.0">parmed</requirement>
9 <requirement type="package" version="2020.4">gromacs</requirement> 9 <requirement type="package" version="2020.4">gromacs</requirement>
10 <requirement type="package" version="2.11.2">jinja2</requirement> 10 <requirement type="package" version="2.11.2">jinja2</requirement>
11 </expand> 11 </expand>
12 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
13 <![CDATA[ 13 <![CDATA[
14 python '$templating_script' '$inputs' && 14 #if $param_inputs.fmt == "GROMACS":
15 PATH_TO_PARMED=\$(dirname `which parmed`) && 15 python '$__tool_directory__/parmconv.py'
16 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) && 16 --istr '$param_inputs.str_in'
17 export GMXDATA=\$AMBERHOME/share/gromacs/top/ && 17 --itop '$param_inputs.top_in'
18 parmed -i ligand.script -O && 18 $param_inputs.modbehaviour.removedihe
19 parmed -i receptor.script -O && 19 $param_inputs.modbehaviour.removebox
20 parmed -i complex.script -O && 20 --iradii '$param_inputs.modbehaviour.radii'
21 parmed -i solvatedcomplex.script -O 21 --istripmask '$stripmask_ligand'
22 22 --o_prmtop '$prmtop_ligand'
23 2>&1 &&
24 python '$__tool_directory__/parmconv.py'
25 --istr '$param_inputs.str_in'
26 --itop '$param_inputs.top_in'
27 $param_inputs.modbehaviour.removedihe
28 $param_inputs.modbehaviour.removebox
29 --iradii '$param_inputs.modbehaviour.radii'
30 --istripmask '$stripmask_receptor'
31 --o_prmtop '$prmtop_receptor'
32 2>&1 &&
33 python '$__tool_directory__/parmconv.py'
34 --istr '$param_inputs.str_in'
35 --itop '$param_inputs.top_in'
36 $param_inputs.modbehaviour.removedihe
37 $param_inputs.modbehaviour.removebox
38 --iradii '$param_inputs.modbehaviour.radii'
39 --istripmask '$stripmask_complex'
40 --o_prmtop '$prmtop_complex'
41 2>&1 &&
42 python '$__tool_directory__/parmconv.py'
43 --istr '$param_inputs.str_in'
44 --itop '$param_inputs.top_in'
45 $param_inputs.modbehaviour.removedihe
46 $param_inputs.modbehaviour.removebox
47 --iradii '$param_inputs.modbehaviour.radii'
48 --istripmask '$stripmask_solvatedcomplex'
49 --o_prmtop '$prmtop_solvatedcomplex'
50 2>&1
51 #else
52 python '$templating_script' '$inputs' &&
53 PATH_TO_PARMED=\$(dirname `which parmed`) &&
54 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
55 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
56 parmed -i ligand.script -O &&
57 parmed -i receptor.script -O &&
58 parmed -i complex.script -O &&
59 parmed -i solvatedcomplex.script -O
60 #end if
23 ]]> 61 ]]>
24 </command> 62 </command>
25 <configfiles> 63 <configfiles>
26 <inputs name="inputs"/> 64 <inputs name="inputs"/>
27 <configfile name="templating_script"> 65 <configfile name="templating_script">
91 ]]> 129 ]]>
92 </configfile> 130 </configfile>
93 </configfiles> 131 </configfiles>
94 <inputs> 132 <inputs>
95 <conditional name="param_inputs"> 133 <conditional name="param_inputs">
96 <param name="fmt" type="select" label="Force Field format"> 134 <param name="fmt" type="select" label="Input format">
97 <option selected="True" value="AMBER">AMBER</option> 135 <option selected="True" value="AMBER">AMBER</option>
98 <option value="GROMACS">GROMACS</option> 136 <option value="GROMACS">GROMACS</option>
99 </param> 137 </param>
100 <when value="AMBER"> 138 <when value="AMBER">
101 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/> 139 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
102 </when> 140 </when>
103 <when value="GROMACS"> 141 <when value="GROMACS">
104 <param name="top_in" type="data" label="Input topology (top) file" format="top"/> 142 <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
105 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/> 143 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
144 <section name="modbehaviour" title="Modify behaviour" expanded="false">
145 <param name="removedihe" type="boolean" truevalue="--removedihe" falsevalue="" checked="false" label="Remove all zero period dihedrals" help="This will remove zero period dihedrals from the generated topology"/>
146 <param name="removebox" type="boolean" truevalue="--removebox" falsevalue="" checked="false" label="Remove periodic box information" help="This will remove periodic information from the generated topology"/>
147 <param name="radii" type="select" label="Radii to use" help="Select the radii to use. Default is mbondi.">
148 <option selected="True" value="mbondi">mbondi</option>
149 <option value="mbondi2">mbondi2</option>
150 <option value="mbondi3">mbondi3</option>
151 <option value="bondi">bondi</option>
152 <option value="amber6">amber6</option>
153 </param>
154 </section>
106 </when> 155 </when>
107 </conditional> 156 </conditional>
108 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand"> 157 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
109 <sanitizer> 158 <sanitizer>
110 <valid initial="string.printable"> 159 <valid initial="string.printable">
111 <remove value="&amp;"/> 160 <add value="&amp;"/>
112 </valid> 161 </valid>
113 <mapping initial="none">
114 <add source="&amp;" target="__and__"/>
115 </mapping>
116 </sanitizer> 162 </sanitizer>
117 </param> 163 </param>
118 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor"> 164 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
119 <sanitizer> 165 <sanitizer>
120 <valid initial="string.printable"> 166 <valid initial="string.printable">
121 <remove value="&amp;"/> 167 <add value="&amp;"/>
122 </valid> 168 </valid>
123 <mapping initial="none">
124 <add source="&amp;" target="__and__"/>
125 </mapping>
126 </sanitizer> 169 </sanitizer>
127 </param> 170 </param>
128 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)"> 171 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
129 <sanitizer> 172 <sanitizer>
130 <valid initial="string.printable"> 173 <valid initial="string.printable">
131 <remove value="&amp;"/> 174 <add value="&amp;"/>
132 </valid> 175 </valid>
133 <mapping initial="none">
134 <add source="&amp;" target="__and__"/>
135 </mapping>
136 </sanitizer> 176 </sanitizer>
137 </param> 177 </param>
138 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)"> 178 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
139 <sanitizer> 179 <sanitizer>
140 <valid initial="string.printable"> 180 <valid initial="string.printable">
141 <remove value="&amp;"/> 181 <add value="&amp;"/>
142 </valid> 182 </valid>
143 <mapping initial="none">
144 <add source="&amp;" target="__and__"/>
145 </mapping>
146 </sanitizer> 183 </sanitizer>
147 </param> 184 </param>
148 </inputs> 185 </inputs>
149 <outputs> 186 <outputs>
150 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/> 187 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
198 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/> 235 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
199 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine --> 236 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
200 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/> 237 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
201 <output name="prmtop_ligand"> 238 <output name="prmtop_ligand">
202 <assert_contents> 239 <assert_contents>
203 <has_text text=" 8 59"/>
204 <has_text text="%FLAG MASS"/> 240 <has_text text="%FLAG MASS"/>
205 <has_text text="CL"/> 241 <has_text text="CL"/>
242 <has_text text="SOLVENT_POINTERS"/>
243 <has_text text="BOX_DIMENSIONS"/>
206 </assert_contents> 244 </assert_contents>
207 </output> 245 </output>
208 <output name="prmtop_receptor"> 246 <output name="prmtop_receptor">
209 <assert_contents> 247 <assert_contents>
210 <has_text text=" 1960 59"/> 248 <has_text text="%FLAG MASS"/>
249 <has_text text="LYS VAL PHE "/>
250 <has_text text="SOLVENT_POINTERS"/>
251 <has_text text="BOX_DIMENSIONS"/>
252 <not_has_text text="CL "/>
253 </assert_contents>
254 </output>
255 <output name="prmtop_solvatedcomplex">
256 <assert_contents>
257 <has_text text="%FLAG MASS"/>
258 <has_text text="LYS VAL PHE"/>
259 <has_text text="SOLVENT_POINTERS"/>
260 <has_text text="BOX_DIMENSIONS"/>
261 </assert_contents>
262 </output>
263 </test>
264 <test>
265 <!-- test with removing dihedrals and periodicity -->
266 <param name="fmt" value="GROMACS"/>
267 <conditional name="param_inputs">
268 <param name="top_in" value="topol_solv.top"/>
269 <param name="str_in" value="solv_ions.gro"/>
270 </conditional>
271 <!-- dihedrals and periodicity -->
272 <param name="removedihe" value="--removedihe"/>
273 <param name="removebox" value="--removebox"/>
274 <!-- pretending CL is a ligand -->
275 <param name="stripmask_ligand" value="!:CL"/>
276 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
277 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
278 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
279 <output name="prmtop_ligand">
280 <assert_contents>
281 <has_text text="%FLAG MASS"/>
282 <has_text text="CL"/>
283 <not_has_text text="SOLVENT_POINTERS"/>
284 <not_has_text text="BOX_DIMENSIONS"/>
285 </assert_contents>
286 </output>
287 <output name="prmtop_receptor">
288 <assert_contents>
211 <has_text text="%FLAG MASS"/> 289 <has_text text="%FLAG MASS"/>
212 <has_text text="LYS VAL PHE "/> 290 <has_text text="LYS VAL PHE "/>
213 <not_has_text text="CL "/> 291 <not_has_text text="CL "/>
292 <not_has_text text="SOLVENT_POINTERS"/>
293 <not_has_text text="BOX_DIMENSIONS"/>
214 </assert_contents> 294 </assert_contents>
215 </output> 295 </output>
216 <output name="prmtop_solvatedcomplex"> 296 <output name="prmtop_solvatedcomplex">
217 <assert_contents> 297 <assert_contents>
218 <has_text text=" 38265 59"/>
219 <has_text text="%FLAG MASS"/> 298 <has_text text="%FLAG MASS"/>
220 <has_text text="LYS VAL PHE"/> 299 <has_text text="LYS VAL PHE"/>
300 <not_has_text text="SOLVENT_POINTERS"/>
301 <not_has_text text="BOX_DIMENSIONS"/>
221 </assert_contents> 302 </assert_contents>
222 </output> 303 </output>
223 </test> 304 </test>
224 </tests> 305 </tests>
225 <help> 306 <help>
226 <![CDATA[ 307 <![CDATA[
227 .. class:: infomark 308 .. class:: infomark
228 309
229 **What it does** 310 **What it does**
230 311
231 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations. 312 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMGBSA/MMPBSA calculations.
232 313
233 .. class:: infomark 314 .. class:: infomark
234 315
235 **How it works** 316 **How it works**
236 317
237 AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user. 318 AmberTools' ParmEd is used to strip unneeded atoms and save the parameter files. The stripmasks are defined by the user.
238 319
239 .. class:: infomark 320 .. class:: infomark
240 321
241 **Outputs created** 322 **Outputs created**
242 323