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 |
|---|---|
| date | Wed, 18 Dec 2019 15:25:39 -0500 |
| parents | 4dba9a5b74fc |
| children | 171ce1253b19 |
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| 3:4dba9a5b74fc | 4:cdaed42b4223 |
|---|---|
| 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 |