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 |
|---|---|
| date | Wed, 20 May 2020 13:00:42 -0400 |
| parents | 171ce1253b19 |
| children | f197e34c33a9 |
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| 8:4b4232c98b6e | 9:a97dcfc23b4b |
|---|---|
| 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 |