Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 9:a97dcfc23b4b draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author | chemteam |
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date | Wed, 20 May 2020 13:00:42 -0400 |
parents | 171ce1253b19 |
children | f197e34c33a9 |
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8:4b4232c98b6e | 9:a97dcfc23b4b |
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1 <tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@.1"> | 1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
2 <description>for system equilibration or data collection</description> | 2 <description>for system equilibration or data collection</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <token name="@GALAXY_VERSION@">0</token> | |
5 </macros> | 6 </macros> |
6 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
8 #if $sets.mdp.mdpfile == "custom": | 9 #if $sets.mdp.mdpfile == "custom": |
9 ln -s '$sets.mdp.mdp_input' ./md.mdp && | 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && |
41 #end if | 42 #end if |
42 -p ./top_input.top | 43 -p ./top_input.top |
43 -o outp.tpr &>> verbose.txt && | 44 -o outp.tpr &>> verbose.txt && |
44 | 45 |
45 | 46 |
46 gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt | 47 gmx mdrun |
47 | 48 -nt "\${GALAXY_SLOTS:-4}" |
49 ## GPU | |
50 #if "\${GROMACS_GPU:-0}" == 1: | |
51 -ntmpi 1 | |
52 -nb gpu | |
53 -pme gpu | |
54 #end if | |
55 -deffnm outp &>> verbose.txt | |
56 | |
48 #if $outps.str == 'pdb' or $outps.str == 'both' | 57 #if $outps.str == 'pdb' or $outps.str == 'both' |
49 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt | 58 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt |
50 #end if | 59 #end if |
51 | 60 |
52 && cat md.mdp &>> verbose.txt | 61 && cat md.mdp &>> verbose.txt |
257 <expand macro="log_outputs" /> | 266 <expand macro="log_outputs" /> |
258 </outputs> | 267 </outputs> |
259 | 268 |
260 <tests> | 269 <tests> |
261 <test expect_num_outputs="3"> | 270 <test expect_num_outputs="3"> |
262 <param name="gro_input" value="npt.gro" /> | 271 <param name="gro_input" value="str_ions.gro" /> |
263 <param name="top_input" value="topol_solv.top" /> | 272 <param name="top_input" value="topol_solv.top" /> |
264 <!-- <param name="cpt_bool" value="yes" /> --> | 273 <!-- <param name="cpt_bool" value="yes" /> --> |
265 <param name="cpt_in" value="npt.cpt" /> | 274 <param name="cpt_in" value="npt.cpt" /> |
266 <param name="mdpfile" value="custom" /> | 275 <param name="mdpfile" value="custom" /> |
267 <param name="mdp_input" value="md.mdp" /> | 276 <param name="mdp_input" value="md.mdp" /> |
269 <param name="traj" value="trr"/> | 278 <param name="traj" value="trr"/> |
270 <param name="str" value="gro"/> | 279 <param name="str" value="gro"/> |
271 <param name="tpr_out" value="true"/> | 280 <param name="tpr_out" value="true"/> |
272 <param name="ensemble" value="npt" /> | 281 <param name="ensemble" value="npt" /> |
273 <!-- <param name="posres_bool" value="false" /> --> | 282 <!-- <param name="posres_bool" value="false" /> --> |
274 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 283 <output name="output1" ftype="gro"> |
275 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 284 <assert_contents> |
276 <output name="output8" file="md_0_1.tpr" ftype="binary" compare="sim_size"/> | 285 <has_size value="6537" /> |
277 <!-- <output name="output1" ftype="gro"> | 286 <has_n_lines n="97" /> |
278 <assert_contents> | 287 <has_line line="TEST in water" /> |
279 <has_size value="2647999" /> | |
280 </assert_contents> | 288 </assert_contents> |
281 </output> | 289 </output> |
282 <output name="output3" ftype="trr"> | 290 <output name="output3" ftype="trr"> |
283 <assert_contents> | 291 <assert_contents> |
284 <has_size value="10132584" /> | 292 <has_size value="26136" /> |
285 </assert_contents> | 293 </assert_contents> |
286 </output> --> | 294 </output> |
295 <output name="output8" ftype="binary"> | |
296 <assert_contents> | |
297 <has_size value="44164" /> | |
298 </assert_contents> | |
299 </output> | |
287 </test> | 300 </test> |
288 | 301 |
289 <test expect_num_outputs="3"> | 302 <test expect_num_outputs="3"> |
290 <param name="gro_input" value="npt.gro" /> | 303 <param name="gro_input" value="str_ions.gro" /> |
291 <param name="top_input" value="topol_solv.top" /> | 304 <param name="top_input" value="topol_solv.top" /> |
292 <!-- <param name="cpt_bool" value="yes" /> --> | 305 <!-- <param name="cpt_bool" value="yes" /> --> |
293 <param name="cpt_in" value="npt.cpt" /> | 306 <param name="cpt_in" value="npt.cpt" /> |
294 <!-- <param name="ndx_bool" value="false" /> --> | 307 <!-- <param name="ndx_bool" value="false" /> --> |
295 <param name="traj" value="trr"/> | 308 <param name="traj" value="trr"/> |
296 <param name="str" value="both"/> | 309 <param name="str" value="both"/> |
297 <expand macro="test_params"/> | 310 <expand macro="test_params"/> |
298 <param name="ensemble" value="npt" /> | 311 <param name="ensemble" value="npt" /> |
299 <!-- <param name="posres_bool" value="false" /> --> | 312 <!-- <param name="posres_bool" value="false" /> --> |
300 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 313 <output name="output1" ftype="gro"> |
301 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 314 <assert_contents> |
302 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 315 <has_size value="6537" /> |
316 <has_n_lines n="97" /> | |
317 <has_line line="TEST in water" /> | |
318 </assert_contents> | |
319 </output> | |
320 <output name="output2" ftype="pdb"> | |
321 <assert_contents> | |
322 <has_size value="7582" /> | |
323 <has_n_lines n="100" /> | |
324 <has_line line="TITLE TEST in water" /> | |
325 <has_line line="REMARK THIS IS A SIMULATION BOX" /> | |
326 </assert_contents> | |
327 </output> | |
328 <output name="output3" ftype="trr"> | |
329 <assert_contents> | |
330 <has_size value="26136" /> | |
331 </assert_contents> | |
332 </output> | |
303 </test> | 333 </test> |
304 | 334 |
305 <test expect_num_outputs="3"> | 335 <test expect_num_outputs="3"> |
306 <param name="gro_input" value="npt.gro" /> | 336 <param name="gro_input" value="str_ions.gro" /> |
307 <param name="top_input" value="topol_solv.top" /> | 337 <param name="top_input" value="topol_solv.top" /> |
308 <!-- <param name="cpt_bool" value="yes" /> --> | 338 <!-- <param name="cpt_bool" value="yes" /> --> |
309 <param name="cpt_in" value="npt.cpt" /> | 339 <param name="cpt_in" value="npt.cpt" /> |
310 <!-- <param name="ndx_bool" value="true" /> --> | 340 <!-- <param name="ndx_bool" value="true" /> --> |
311 <param name="ndx_in" value="index.ndx" /> | 341 <param name="ndx_in" value="index.ndx" /> |
312 <param name="traj" value="trr"/> | 342 <param name="traj" value="trr"/> |
313 <param name="str" value="both"/> | 343 <param name="str" value="both"/> |
314 <expand macro="test_params"/> | 344 <expand macro="test_params"/> |
315 <param name="ensemble" value="npt" /> | 345 <param name="ensemble" value="npt" /> |
316 <!-- <param name="posres_bool" value="false" /> --> | 346 <!-- <param name="posres_bool" value="false" /> --> |
317 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> | 347 <output name="output1" ftype="gro" compare="sim_size"> |
318 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> | 348 <assert_contents> |
319 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> | 349 <has_size value="6537" /> |
350 <has_n_lines n="97" /> | |
351 <has_line line="TEST in water" /> | |
352 </assert_contents> | |
353 </output> | |
354 <output name="output2" ftype="pdb" compare="sim_size"> | |
355 <assert_contents> | |
356 <has_size value="7582" /> | |
357 <has_n_lines n="100" /> | |
358 <has_line line="TITLE TEST in water" /> | |
359 <has_line line="REMARK THIS IS A SIMULATION BOX" /> | |
360 </assert_contents> | |
361 </output> | |
362 <output name="output3" ftype="trr" compare="sim_size"> | |
363 <assert_contents> | |
364 <has_size value="26136" /> | |
365 </assert_contents> | |
366 </output> | |
320 </test> | 367 </test> |
321 | 368 |
322 <test expect_num_outputs="3"> | 369 <test expect_num_outputs="3"> |
323 <param name="gro_input" value="em.gro" /> | 370 <param name="gro_input" value="str_ions.gro" /> |
324 <param name="top_input" value="topol_solv.top" /> | 371 <param name="top_input" value="topol_solv.top" /> |
325 <!-- <param name="posres_bool" value="true" /> --> | 372 <!-- <param name="posres_bool" value="true" /> --> |
326 <param name="itp_in" value="posres.itp" /> | 373 <param name="itp_in" value="posres.itp" /> |
327 <!-- <param name="cpt_bool" value="no" /> --> | 374 <!-- <param name="cpt_bool" value="no" /> --> |
328 <param name="cpt_out" value="true" /> | 375 <param name="cpt_out" value="true" /> |
330 <param name="traj" value="xtc"/> | 377 <param name="traj" value="xtc"/> |
331 <param name="str" value="pdb"/> | 378 <param name="str" value="pdb"/> |
332 <param name="ensemble" value="nvt" /> | 379 <param name="ensemble" value="nvt" /> |
333 <expand macro="test_params"/> | 380 <expand macro="test_params"/> |
334 | 381 |
335 <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> | 382 <output name="output2" ftype="pdb"> |
336 <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> | 383 <assert_contents> |
337 <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> | 384 <has_size value="7582" /> |
385 <has_n_lines n="100" /> | |
386 <has_line line="TITLE TEST in water" /> | |
387 <has_line line="REMARK THIS IS A SIMULATION BOX" /> | |
388 </assert_contents> | |
389 </output> | |
390 <output name="output4" ftype="xtc"> | |
391 <assert_contents> | |
392 <has_size value="4910" delta="20"/> | |
393 </assert_contents> | |
394 </output> | |
395 <output name="output5" ftype="cpt"> | |
396 <assert_contents> | |
397 <has_size value="3350" delta="20"/> | |
398 </assert_contents> | |
399 </output> | |
338 </test> | 400 </test> |
339 </tests> | 401 </tests> |
340 | 402 |
341 <help><![CDATA[ | 403 <help><![CDATA[ |
342 | 404 |