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comparison sim.xml @ 13:da8753545526 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
author chemteam
date Wed, 29 Sep 2021 07:40:59 +0000
parents 73008ef1f487
children 525ca7c8065f
comparison
equal deleted inserted replaced
12:73008ef1f487 13:da8753545526
232 232
233 <expand macro="log" /> 233 <expand macro="log" />
234 234
235 </inputs> 235 </inputs>
236 <outputs> 236 <outputs>
237 <data name="output1" format="gro" from_work_dir="outp.gro"> 237 <data name="output1" format="gro" from_work_dir="outp.gro" label="GROMACS simulation (GRO) on ${on_string}">
238 <filter>outps["str"] == 'gro' or outps["str"] == 'both'</filter> 238 <filter>outps["str"] == 'gro' or outps["str"] == 'both'</filter>
239 </data> 239 </data>
240 <data name="output2" format="pdb" from_work_dir="outp.pdb"> 240 <data name="output2" format="pdb" from_work_dir="outp.pdb" label="GROMACS simulation (PDB) file on ${on_string}">
241 <filter>outps["str"] == 'pdb' or outps["str"] == 'both'</filter> 241 <filter>outps["str"] == 'pdb' or outps["str"] == 'both'</filter>
242 </data> 242 </data>
243 <data name="output3" format="trr" from_work_dir="outp.trr"> 243 <data name="output3" format="trr" from_work_dir="outp.trr" label="GROMACS simulation (TRR) on ${on_string}">
244 <filter>outps["traj"] == 'trr' or outps["traj"] == 'both'</filter> 244 <filter>outps["traj"] == 'trr' or outps["traj"] == 'both'</filter>
245 </data> 245 </data>
246 <data name="output4" format="xtc" from_work_dir="outp.xtc"> 246 <data name="output4" format="xtc" from_work_dir="outp.xtc" label="GROMACS simulation (XTC) on ${on_string}">
247 <filter>outps["traj"] == 'xtc' or outps["traj"] == 'both'</filter> 247 <filter>outps["traj"] == 'xtc' or outps["traj"] == 'both'</filter>
248 </data> 248 </data>
249 <data name="output5" format="cpt" from_work_dir="outp.cpt"> 249 <data name="output5" format="cpt" from_work_dir="outp.cpt" label="GROMACS simulation (CPT) on ${on_string}">
250 <filter>outps["cpt_out"] == 'true'</filter> 250 <filter>outps["cpt_out"] == 'true'</filter>
251 </data> 251 </data>
252 <data name="output6" format="edr" from_work_dir="outp.edr"> 252 <data name="output6" format="edr" from_work_dir="outp.edr" label="GROMACS simulation (EDR) on ${on_string}">
253 <filter>outps["edr_out"] == 'true'</filter> 253 <filter>outps["edr_out"] == 'true'</filter>
254 </data> 254 </data>
255 <data name="output7" format="xvg" from_work_dir="outp_pullf.xvg"> 255 <data name="output7" format="xvg" from_work_dir="outp_pullf.xvg" label="GROMACS simulation (XVG) on ${on_string}">
256 <filter>outps["xvg_out"] == 'true'</filter> 256 <filter>outps["xvg_out"] == 'true'</filter>
257 </data> 257 </data>
258 <data name="output7_1" format="xvg" from_work_dir="outp.xvg"> 258 <data name="output7_1" format="xvg" from_work_dir="outp.xvg">
259 <filter>outps["xvg_out"] == 'true'</filter> 259 <filter>outps["xvg_out"] == 'true'</filter>
260 </data> 260 </data>
261 <!-- <collection name="output7" type="list"> 261 <!-- <collection name="output7" type="list">
262 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.xvg" visible="true" directory="." /> 262 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.xvg" visible="true" directory="." />
263 <filter>outps["xvg_out"] == 'true'</filter> 263 <filter>outps["xvg_out"] == 'true'</filter>
264 </collection> --> 264 </collection> -->
265 <data name="output8" format="binary" from_work_dir="outp.tpr"> 265 <data name="output8" format="tpr" from_work_dir="outp.tpr">
266 <filter>outps["tpr_out"] == 'true'</filter> 266 <filter>outps["tpr_out"] == 'true'</filter>
267 </data> 267 </data>
268 268
269 <expand macro="log_outputs" /> 269 <expand macro="log_outputs" />
270 </outputs> 270 </outputs>
271 271
272 <tests> 272 <tests>
273 <test expect_num_outputs="3"> 273 <test expect_num_outputs="3">
274 <param name="gro_input" value="str_ions.gro" /> 274 <param name="gro_input" value="str_ions.gro" />
275 <param name="top_input" value="topol_solv.top" /> 275 <param name="top_input" value="topol_md.top" />
276 <!-- <param name="cpt_bool" value="yes" /> --> 276 <!-- <param name="cpt_bool" value="yes" /> -->
277 <param name="cpt_in" value="npt.cpt" /> 277 <param name="cpt_in" value="npt.cpt" />
278 <param name="mdpfile" value="custom" /> 278 <param name="mdpfile" value="custom" />
279 <param name="mdp_input" value="md.mdp" /> 279 <param name="mdp_input" value="md.mdp" />
280 <!-- <param name="ndx_bool" value="false" /> --> 280 <!-- <param name="ndx_bool" value="false" /> -->
293 <output name="output3" ftype="trr"> 293 <output name="output3" ftype="trr">
294 <assert_contents> 294 <assert_contents>
295 <has_size value="26136" /> 295 <has_size value="26136" />
296 </assert_contents> 296 </assert_contents>
297 </output> 297 </output>
298 <output name="output8" ftype="binary"> 298 <output name="output8" ftype="tpr">
299 <assert_contents> 299 <assert_contents>
300 <has_size value="44164" /> 300 <has_size value="44212" />
301 </assert_contents> 301 </assert_contents>
302 </output> 302 </output>
303 </test> 303 </test>
304 304
305 <test expect_num_outputs="3"> 305 <test expect_num_outputs="3">
306 <param name="gro_input" value="str_ions.gro" /> 306 <param name="gro_input" value="str_ions.gro" />
307 <param name="top_input" value="topol_solv.top" /> 307 <param name="top_input" value="topol_md.top" />
308 <!-- <param name="cpt_bool" value="yes" /> --> 308 <!-- <param name="cpt_bool" value="yes" /> -->
309 <param name="cpt_in" value="npt.cpt" /> 309 <param name="cpt_in" value="npt.cpt" />
310 <!-- <param name="ndx_bool" value="false" /> --> 310 <!-- <param name="ndx_bool" value="false" /> -->
311 <param name="traj" value="trr"/> 311 <param name="traj" value="trr"/>
312 <param name="str" value="both"/> 312 <param name="str" value="both"/>
335 </output> 335 </output>
336 </test> 336 </test>
337 337
338 <test expect_num_outputs="3"> 338 <test expect_num_outputs="3">
339 <param name="gro_input" value="str_ions.gro" /> 339 <param name="gro_input" value="str_ions.gro" />
340 <param name="top_input" value="topol_solv.top" /> 340 <param name="top_input" value="topol_md.top" />
341 <!-- <param name="cpt_bool" value="yes" /> --> 341 <!-- <param name="cpt_bool" value="yes" /> -->
342 <param name="cpt_in" value="npt.cpt" /> 342 <param name="cpt_in" value="npt.cpt" />
343 <!-- <param name="ndx_bool" value="true" /> --> 343 <!-- <param name="ndx_bool" value="true" /> -->
344 <param name="ndx_in" value="index.ndx" /> 344 <param name="ndx_in" value="index.ndx" />
345 <param name="traj" value="trr"/> 345 <param name="traj" value="trr"/>
346 <param name="str" value="both"/> 346 <param name="str" value="both"/>
347 <expand macro="test_params"/> 347 <expand macro="test_params"/>
348 <param name="ensemble" value="npt" /> 348 <param name="ensemble" value="npt" />
349 <!-- <param name="posres_bool" value="false" /> --> 349 <!-- <param name="posres_bool" value="false" /> -->
350 <output name="output1" ftype="gro" compare="sim_size"> 350 <output name="output1" ftype="gro">
351 <assert_contents> 351 <assert_contents>
352 <has_size value="6537" /> 352 <has_size value="6537" />
353 <has_n_lines n="97" /> 353 <has_n_lines n="97" />
354 <has_line line="TEST in water" /> 354 </assert_contents>
355 </assert_contents> 355 </output>
356 </output> 356 <output name="output2" ftype="pdb">
357 <output name="output2" ftype="pdb" compare="sim_size">
358 <assert_contents> 357 <assert_contents>
359 <has_size value="7582" /> 358 <has_size value="7582" />
360 <has_n_lines n="100" /> 359 <has_n_lines n="100" />
361 <has_line line="TITLE TEST in water" /> 360 <has_line line="TITLE TEST in water" />
362 <has_line line="REMARK THIS IS A SIMULATION BOX" /> 361 <has_line line="REMARK THIS IS A SIMULATION BOX" />
363 </assert_contents> 362 </assert_contents>
364 </output> 363 </output>
365 <output name="output3" ftype="trr" compare="sim_size"> 364 <output name="output3" ftype="trr">
366 <assert_contents> 365 <assert_contents>
367 <has_size value="26136" /> 366 <has_size value="26136" />
368 </assert_contents> 367 </assert_contents>
369 </output> 368 </output>
370 </test> 369 </test>
371
372 <test expect_num_outputs="3"> 370 <test expect_num_outputs="3">
373 <param name="gro_input" value="str_ions.gro" /> 371 <param name="gro_input" value="str_ions.gro" />
374 <param name="top_input" value="topol_solv.top" /> 372 <param name="top_input" value="topol_md.top" />
375 <!-- <param name="posres_bool" value="true" /> --> 373 <!-- <param name="posres_bool" value="true" /> -->
376 <param name="itp_in" value="posres.itp" /> 374 <param name="itp_in" value="posres.itp" />
377 <!-- <param name="cpt_bool" value="no" /> --> 375 <!-- <param name="cpt_bool" value="no" /> -->
378 <param name="cpt_out" value="true" /> 376 <param name="cpt_out" value="true" />
379 <!-- <param name="ndx_bool" value="false" /> --> 377 <!-- <param name="ndx_bool" value="false" /> -->
380 <param name="traj" value="xtc"/> 378 <param name="traj" value="xtc"/>
381 <param name="str" value="pdb"/> 379 <param name="str" value="pdb"/>
382 <param name="ensemble" value="nvt" /> 380 <param name="ensemble" value="nvt" />
383 <expand macro="test_params"/> 381 <expand macro="test_params"/>
384 382
385 <output name="output2" ftype="pdb"> 383 <output name="output2" ftype="pdb">
386 <assert_contents> 384 <assert_contents>
387 <has_size value="7582" /> 385 <has_size value="7582" />
388 <has_n_lines n="100" /> 386 <has_n_lines n="100" />
389 <has_line line="TITLE TEST in water" /> 387 <has_line line="TITLE TEST in water" />