Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 4:cdaed42b4223 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1"
author | chemteam |
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date | Wed, 18 Dec 2019 15:25:39 -0500 |
parents | 4dba9a5b74fc |
children | 171ce1253b19 |
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3:4dba9a5b74fc | 4:cdaed42b4223 |
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3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 | |
9 #if $sets.mdp.mdpfile == "custom": | 8 #if $sets.mdp.mdpfile == "custom": |
10 ln -s '$sets.mdp.mdp_input' ./md.mdp && | 9 ln -s '$sets.mdp.mdp_input' ./md.mdp && |
11 #end if | 10 #end if |
12 #if $sets.mdp.mdpfile == "default": | 11 #if $sets.mdp.mdpfile == "default": |
13 ln -s '$md' ./md.mdp && | 12 ln -s '$md' ./md.mdp && |
201 <!-- XVG out --> | 200 <!-- XVG out --> |
202 <param name="xvg_out" type="select" label="Produce XVG output" help="Produce tabular XVG file (e.g. forces from pulling simulations)" > | 201 <param name="xvg_out" type="select" label="Produce XVG output" help="Produce tabular XVG file (e.g. forces from pulling simulations)" > |
203 <option value="true">Produce XVG output</option> | 202 <option value="true">Produce XVG output</option> |
204 <option value="false" selected="true">No XVG output</option> | 203 <option value="false" selected="true">No XVG output</option> |
205 </param> | 204 </param> |
205 | |
206 <!-- TPR out --> | |
207 <param name="tpr_out" type="select" label="Produce TPR output" help="Produce TPR binary file" > | |
208 <option value="true">Produce TPR output</option> | |
209 <option value="false" selected="true">No TPR output</option> | |
210 </param> | |
206 | 211 |
207 </section> | 212 </section> |
208 | 213 |
209 <section name="sets" title="Settings" expanded="false"> | 214 <section name="sets" title="Settings" expanded="false"> |
210 <!-- other ... --> | 215 <!-- other ... --> |
219 <expand macro="log" /> | 224 <expand macro="log" /> |
220 | 225 |
221 </inputs> | 226 </inputs> |
222 <outputs> | 227 <outputs> |
223 <data name="output1" format="gro" from_work_dir="outp.gro"> | 228 <data name="output1" format="gro" from_work_dir="outp.gro"> |
224 <filter>outps.str == 'gro' or outps.str == 'both'</filter> | 229 <filter>outps["str"] == 'gro' or outps["str"] == 'both'</filter> |
225 </data> | 230 </data> |
226 <data name="output2" format="pdb" from_work_dir="outp.pdb"> | 231 <data name="output2" format="pdb" from_work_dir="outp.pdb"> |
227 <filter>outps.str == 'pdb' or outps.str == 'both'</filter> | 232 <filter>outps["str"] == 'pdb' or outps["str"] == 'both'</filter> |
228 </data> | 233 </data> |
229 <data name="output3" format="trr" from_work_dir="outp.trr"> | 234 <data name="output3" format="trr" from_work_dir="outp.trr"> |
230 <filter>outps.traj == 'trr' or outps.traj == 'both'</filter> | 235 <filter>outps["traj"] == 'trr' or outps["traj"] == 'both'</filter> |
231 </data> | 236 </data> |
232 <data name="output4" format="xtc" from_work_dir="outp.xtc"> | 237 <data name="output4" format="xtc" from_work_dir="outp.xtc"> |
233 <filter>outps.traj == 'xtc' or outps.traj == 'both'</filter> | 238 <filter>outps["traj"] == 'xtc' or outps["traj"] == 'both'</filter> |
234 </data> | 239 </data> |
235 <data name="output5" format="cpt" from_work_dir="outp.cpt"> | 240 <data name="output5" format="cpt" from_work_dir="outp.cpt"> |
236 <filter>outps.cpt_out == 'true'</filter> | 241 <filter>outps["cpt_out"] == 'true'</filter> |
237 </data> | 242 </data> |
238 <data name="output6" format="edr" from_work_dir="outp.edr"> | 243 <data name="output6" format="edr" from_work_dir="outp.edr"> |
239 <filter>outps.edr_out == 'true'</filter> | 244 <filter>outps["edr_out"] == 'true'</filter> |
240 </data> | 245 </data> |
241 <collection name="output7" type="list"> | 246 <collection name="output7" type="list"> |
242 <discover_datasets pattern="(?P<designation>.*)\.xvg" visible="true" directory="." /> | 247 <discover_datasets pattern="(?P<designation>.*)\.xvg" visible="true" directory="." /> |
243 <filter>outps.xvg_out == 'true'</filter> | 248 <filter>outps["xvg_out"] == 'true'</filter> |
244 </collection> | 249 </collection> |
250 <data name="output8" format="binary" from_work_dir="outp.tpr"> | |
251 <filter>outps["tpr_out"] == 'true'</filter> | |
252 </data> | |
245 | 253 |
246 <expand macro="log_outputs" /> | 254 <expand macro="log_outputs" /> |
247 </outputs> | 255 </outputs> |
248 | 256 |
249 <tests> | 257 <tests> |
250 <test> | 258 <test expect_num_outputs="3"> |
251 <param name="gro_input" value="npt.gro" /> | 259 <param name="gro_input" value="npt.gro" /> |
252 <param name="top_input" value="topol_solv.top" /> | 260 <param name="top_input" value="topol_solv.top" /> |
253 <!-- <param name="cpt_bool" value="yes" /> --> | 261 <!-- <param name="cpt_bool" value="yes" /> --> |
254 <param name="cpt_in" value="npt.cpt" /> | 262 <param name="cpt_in" value="npt.cpt" /> |
255 <param name="mdpfile" value="custom" /> | 263 <param name="mdpfile" value="custom" /> |
256 <param name="mdp_input" value="md.mdp" /> | 264 <param name="mdp_input" value="md.mdp" /> |
257 <!-- <param name="ndx_bool" value="false" /> --> | 265 <!-- <param name="ndx_bool" value="false" /> --> |
258 <param name="traj" value="trr"/> | 266 <param name="traj" value="trr"/> |
259 <param name="str" value="gro"/> | 267 <param name="str" value="gro"/> |
268 <param name="tpr_out" value="true"/> | |
260 <param name="ensemble" value="npt" /> | 269 <param name="ensemble" value="npt" /> |
261 <!-- <param name="posres_bool" value="false" /> --> | 270 <!-- <param name="posres_bool" value="false" /> --> |
262 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 271 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
263 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 272 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
273 <output name="output8" file="md_0_1.tpr" ftype="binary" compare="sim_size"/> | |
264 <!-- <output name="output1" ftype="gro"> | 274 <!-- <output name="output1" ftype="gro"> |
265 <assert_contents> | 275 <assert_contents> |
266 <has_size value="2647999" /> | 276 <has_size value="2647999" /> |
267 </assert_contents> | 277 </assert_contents> |
268 </output> | 278 </output> |
271 <has_size value="10132584" /> | 281 <has_size value="10132584" /> |
272 </assert_contents> | 282 </assert_contents> |
273 </output> --> | 283 </output> --> |
274 </test> | 284 </test> |
275 | 285 |
276 <test> | 286 <test expect_num_outputs="3"> |
277 <param name="gro_input" value="npt.gro" /> | 287 <param name="gro_input" value="npt.gro" /> |
278 <param name="top_input" value="topol_solv.top" /> | 288 <param name="top_input" value="topol_solv.top" /> |
279 <!-- <param name="cpt_bool" value="yes" /> --> | 289 <!-- <param name="cpt_bool" value="yes" /> --> |
280 <param name="cpt_in" value="npt.cpt" /> | 290 <param name="cpt_in" value="npt.cpt" /> |
281 <!-- <param name="ndx_bool" value="false" /> --> | 291 <!-- <param name="ndx_bool" value="false" /> --> |
287 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 297 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
288 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 298 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> |
289 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 299 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
290 </test> | 300 </test> |
291 | 301 |
292 <test> | 302 <test expect_num_outputs="3"> |
293 <param name="gro_input" value="npt.gro" /> | 303 <param name="gro_input" value="npt.gro" /> |
294 <param name="top_input" value="topol_solv.top" /> | 304 <param name="top_input" value="topol_solv.top" /> |
295 <!-- <param name="cpt_bool" value="yes" /> --> | 305 <!-- <param name="cpt_bool" value="yes" /> --> |
296 <param name="cpt_in" value="npt.cpt" /> | 306 <param name="cpt_in" value="npt.cpt" /> |
297 <!-- <param name="ndx_bool" value="true" /> --> | 307 <!-- <param name="ndx_bool" value="true" /> --> |
304 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 314 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> |
305 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 315 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> |
306 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 316 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> |
307 </test> | 317 </test> |
308 | 318 |
309 <test> | 319 <test expect_num_outputs="3"> |
310 <param name="gro_input" value="em.gro" /> | 320 <param name="gro_input" value="em.gro" /> |
311 <param name="top_input" value="topol_solv.top" /> | 321 <param name="top_input" value="topol_solv.top" /> |
312 <!-- <param name="posres_bool" value="true" /> --> | 322 <!-- <param name="posres_bool" value="true" /> --> |
313 <param name="itp_in" value="posres.itp" /> | 323 <param name="itp_in" value="posres.itp" /> |
314 <!-- <param name="cpt_bool" value="no" /> --> | 324 <!-- <param name="cpt_bool" value="no" /> --> |
320 <expand macro="test_params"/> | 330 <expand macro="test_params"/> |
321 | 331 |
322 <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> | 332 <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> |
323 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> | 333 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> |
324 <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> | 334 <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> |
325 | |
326 </test> | 335 </test> |
327 </tests> | 336 </tests> |
328 | 337 |
329 <help><![CDATA[ | 338 <help><![CDATA[ |
330 | 339 |