| Previous changeset 1:ec3f665cca3e (2019-10-30) Next changeset 3:4dba9a5b74fc (2019-12-01) |
|
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" |
|
modified:
macros.xml sim.xml |
|
added:
test-data/md_0_1.ndx test-data/md_0_1.xvg test-data/posre_cl.itp |
| b |
| diff -r ec3f665cca3e -r 5642f48f5698 macros.xml --- a/macros.xml Wed Oct 30 13:34:07 2019 -0400 +++ b/macros.xml Wed Nov 20 11:13:22 2019 -0500 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2019.1.2</token> + <token name="@VERSION@">2019.1.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="2019.1">gromacs</requirement> @@ -11,19 +11,6 @@ </citations> </xml> <xml name="md_inputs"> - <param argument="traj" type="select" label="Trajectory output"> - <option value='none'>Return no trajectory output</option> - <option value='xtc'>Return .xtc file (reduced precision)</option> - <option value='trr'>Return .trr file (full precision)</option> - <option value='both'>Return both .xtc and .trr files</option> - </param> - - <param argument="str" type="select" label="Structure output"> - <option value='none'>Return no structure output</option> - <option value='gro'>Return .gro file</option> - <option value='pdb'>Return .pdb file</option> - <option value='both'>Return both .gro and .pdb files</option> - </param> <conditional name="mdp"> <param name="mdpfile" type="select" label="Parameter input"> @@ -73,6 +60,15 @@ </xml> + <xml name="log"> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> + </xml> + + <xml name="log_outputs"> + <data name="report" format="txt" from_work_dir="verbose.txt"> + <filter>capture_log</filter> + </data> + </xml> <xml name="test_params"> <param name="mdpfile" value="default" /> |
| b |
| diff -r ec3f665cca3e -r 5642f48f5698 sim.xml --- a/sim.xml Wed Oct 30 13:34:07 2019 -0400 +++ b/sim.xml Wed Nov 20 11:13:22 2019 -0500 |
| [ |
| b'@@ -5,47 +5,48 @@\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n- #if $mdp.mdpfile == "custom":\n- ln -s \'$mdp.mdp_input\' ./md.mdp &&\n+\n+ #if $sets.mdp.mdpfile == "custom":\n+ ln -s \'$sets.mdp.mdp_input\' ./md.mdp &&\n #end if\n- #if $mdp.mdpfile == "default":\n+ #if $sets.mdp.mdpfile == "default":\n ln -s \'$md\' ./md.mdp &&\n #end if\n \n ln -s \'$gro_input\' ./inp.gro &&\n ln -s \'$top_input\' ./top_input.top &&\n \n- #if $posres.posres_bool == "true":\n- ln -s \'$posres.itp_inp\' ./posres.itp &&\n- #end if\n- \n- #if $cpt_inp.cpt_bool == "yes":\n- ln -s \'$cpt_inp.cpt_in\' ./inp.cpt &&\n+ #if $inps.itp_in:\n+ ln -s \'$inps.itp_in\' ./posres.itp &&\n #end if\n \n- #if $ndx_inp.ndx_bool == "yes":\n- ln -s \'$ndx_inp.ndx_in\' ./index.ndx &&\n+ #if $inps.cpt_in:\n+ ln -s \'$inps.cpt_in\' ./inp.cpt &&\n+ #end if\n+\n+ #if $inps.ndx_in:\n+ ln -s \'$inps.ndx_in\' ./index.ndx &&\n #end if\n \n gmx grompp \n -f ./md.mdp \n -c ./inp.gro \n- #if $cpt_inp.cpt_bool == "yes":\n- -t ./inp.cpt \n+ #if $inps.cpt_in:\n+ -t ./inp.cpt\n #end if\n- #if $posres.posres_bool == "true":\n+ #if $inps.itp_in:\n -r ./inp.gro\n #end if\n- #if $ndx_inp.ndx_bool == "true":\n+ #if $inps.ndx_in:\n -n ./index.ndx\n #end if\n -p ./top_input.top \n -o outp.tpr &>> verbose.txt &&\n- \n- \n+\n+\n gmx mdrun -deffnm outp &>> verbose.txt\n \n- #if $str == \'pdb\' or $str == \'both\'\n+ #if $outps.str == \'pdb\' or $outps.str == \'both\'\n && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt\n #end if\n \n@@ -55,42 +56,44 @@\n <configfiles>\n <!-- .mdp file for the gromacs simulation -->\n <configfile name="md">\n- #if $mdp.mdpfile == \'default\':\n+ #if $sets.mdp.mdpfile == \'default\':\n title = OPLS Lysozyme MD simulation \n ; Run parameters\n- integrator = $mdp.integrator ; leap-frog integrator\n- nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns)\n- dt = $mdp.step_length ; 2 fs\n+ integrator = $sets.mdp.integrator ; leap-frog integrator\n+ nsteps = $sets.mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns)\n+ dt = $sets.mdp.step_length ; 2 fs\n ; Output control\n- nstxout = $mdp.write_freq ; save coordinates every 10.0 ps\n- nstvout = $mdp.write_freq ; save velocities every 10.0 ps\n- nstenergy = $mdp.write_freq ; save energies every 10.0 ps\n- nstlog = $mdp.write_freq ; update log file every 10.0 ps\n- nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps\n+ nstxout = $sets.mdp.write_freq ; save coordinates every 10.0 ps\n+ nstvout = $sets.mdp.write_freq ; save velocities every 10.0 ps\n+ nstenergy = $sets.mdp.write_freq ; save energies every 10.0 ps\n+ nstlog = $sets.mdp.write_freq ; update log file every 10.0 ps\n+ nstxout-compressed = $sets.mdp.write_freq ; save compressed coordinates every 10.0 ps\n ; nstxout-compressed replaces nstxtcout\n compressed-x-grps = System ; group(s) to write to the compressed trajectory file\n '..b'm name="cpt_bool" value="yes" /> -->\n <param name="cpt_in" value="npt.cpt" />\n <param name="mdpfile" value="custom" />\n <param name="mdp_input" value="md.mdp" />\n- <param name="ndx_bool" value="no" />\n+ <!-- <param name="ndx_bool" value="false" /> -->\n <param name="traj" value="trr"/>\n <param name="str" value="gro"/>\n <param name="ensemble" value="npt" />\n- <param name="posres_bool" value="false" />\n+ <!-- <param name="posres_bool" value="false" /> -->\n <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>\n <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>\n+ <!-- <output name="output1" ftype="gro">\n+ <assert_contents>\n+ <has_size value="2647999" />\n+ </assert_contents>\n+ </output>\n+ <output name="output3" ftype="trr">\n+ <assert_contents>\n+ <has_size value="10132584" />\n+ </assert_contents>\n+ </output> -->\n </test>\n \n <test>\n <param name="gro_input" value="npt.gro" />\n <param name="top_input" value="topol_solv.top" />\n- <param name="cpt_bool" value="yes" />\n+ <!-- <param name="cpt_bool" value="yes" /> -->\n <param name="cpt_in" value="npt.cpt" />\n- <param name="ndx_bool" value="no" />\n+ <!-- <param name="ndx_bool" value="false" /> -->\n <param name="traj" value="trr"/>\n <param name="str" value="both"/>\n <expand macro="test_params"/>\n <param name="ensemble" value="npt" />\n- <param name="posres_bool" value="false" />\n+ <!-- <param name="posres_bool" value="false" /> -->\n <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>\n <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>\n <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>\n@@ -222,15 +292,15 @@\n <test>\n <param name="gro_input" value="npt.gro" />\n <param name="top_input" value="topol_solv.top" />\n- <param name="cpt_bool" value="yes" />\n+ <!-- <param name="cpt_bool" value="yes" /> -->\n <param name="cpt_in" value="npt.cpt" />\n- <param name="ndx_bool" value="yes" />\n+ <!-- <param name="ndx_bool" value="true" /> -->\n <param name="ndx_in" value="index.ndx" />\n <param name="traj" value="trr"/>\n <param name="str" value="both"/>\n <expand macro="test_params"/>\n <param name="ensemble" value="npt" />\n- <param name="posres_bool" value="false" />\n+ <!-- <param name="posres_bool" value="false" /> -->\n <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>\n <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>\n <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>\n@@ -239,11 +309,11 @@\n <test>\n <param name="gro_input" value="em.gro" />\n <param name="top_input" value="topol_solv.top" />\n- <param name="posres_bool" value="true" />\n- <param name="itp_inp" value="posres.itp" />\n- <param name="cpt_bool" value="no" />\n+ <!-- <param name="posres_bool" value="true" /> -->\n+ <param name="itp_in" value="posres.itp" />\n+ <!-- <param name="cpt_bool" value="no" /> -->\n <param name="cpt_out" value="true" />\n- <param name="ndx_bool" value="no" />\n+ <!-- <param name="ndx_bool" value="false" /> -->\n <param name="traj" value="xtc"/>\n <param name="str" value="pdb"/>\n <param name="ensemble" value="nvt" />\n' |
| b |
| diff -r ec3f665cca3e -r 5642f48f5698 test-data/md_0_1.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.ndx Wed Nov 20 11:13:22 2019 -0500 |
| [ |
| b'@@ -0,0 +1,13032 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30\n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45\n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60\n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75\n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105\n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120\n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135\n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150\n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165\n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195\n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210\n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225\n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240\n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255\n+ 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270\n+ 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285\n+ 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300\n+ 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315\n+ 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330\n+ 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345\n+ 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360\n+ 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375\n+ 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390\n+ 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405\n+ 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420\n+ 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435\n+ 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450\n+ 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465\n+ 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480\n+ 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495\n+ 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510\n+ 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525\n+ 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540\n+ 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555\n+ 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570\n+ 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585\n+ 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600\n+ 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615\n+ 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630\n+ 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645\n+ 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660\n+ 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675\n+ 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690\n+ 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705\n+ 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720\n+ 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735\n+ 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750\n+ 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765\n+ 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780\n+ 781 782 783'..b'7730 37731 37732 37733 37734 37735\n+37736 37737 37738 37739 37740 37741 37742 37743 37744 37745 37746 37747 37748 37749 37750\n+37751 37752 37753 37754 37755 37756 37757 37758 37759 37760 37761 37762 37763 37764 37765\n+37766 37767 37768 37769 37770 37771 37772 37773 37774 37775 37776 37777 37778 37779 37780\n+37781 37782 37783 37784 37785 37786 37787 37788 37789 37790 37791 37792 37793 37794 37795\n+37796 37797 37798 37799 37800 37801 37802 37803 37804 37805 37806 37807 37808 37809 37810\n+37811 37812 37813 37814 37815 37816 37817 37818 37819 37820 37821 37822 37823 37824 37825\n+37826 37827 37828 37829 37830 37831 37832 37833 37834 37835 37836 37837 37838 37839 37840\n+37841 37842 37843 37844 37845 37846 37847 37848 37849 37850 37851 37852 37853 37854 37855\n+37856 37857 37858 37859 37860 37861 37862 37863 37864 37865 37866 37867 37868 37869 37870\n+37871 37872 37873 37874 37875 37876 37877 37878 37879 37880 37881 37882 37883 37884 37885\n+37886 37887 37888 37889 37890 37891 37892 37893 37894 37895 37896 37897 37898 37899 37900\n+37901 37902 37903 37904 37905 37906 37907 37908 37909 37910 37911 37912 37913 37914 37915\n+37916 37917 37918 37919 37920 37921 37922 37923 37924 37925 37926 37927 37928 37929 37930\n+37931 37932 37933 37934 37935 37936 37937 37938 37939 37940 37941 37942 37943 37944 37945\n+37946 37947 37948 37949 37950 37951 37952 37953 37954 37955 37956 37957 37958 37959 37960\n+37961 37962 37963 37964 37965 37966 37967 37968 37969 37970 37971 37972 37973 37974 37975\n+37976 37977 37978 37979 37980 37981 37982 37983 37984 37985 37986 37987 37988 37989 37990\n+37991 37992 37993 37994 37995 37996 37997 37998 37999 38000 38001 38002 38003 38004 38005\n+38006 38007 38008 38009 38010 38011 38012 38013 38014 38015 38016 38017 38018 38019 38020\n+38021 38022 38023 38024 38025 38026 38027 38028 38029 38030 38031 38032 38033 38034 38035\n+38036 38037 38038 38039 38040 38041 38042 38043 38044 38045 38046 38047 38048 38049 38050\n+38051 38052 38053 38054 38055 38056 38057 38058 38059 38060 38061 38062 38063 38064 38065\n+38066 38067 38068 38069 38070 38071 38072 38073 38074 38075 38076 38077 38078 38079 38080\n+38081 38082 38083 38084 38085 38086 38087 38088 38089 38090 38091 38092 38093 38094 38095\n+38096 38097 38098 38099 38100 38101 38102 38103 38104 38105 38106 38107 38108 38109 38110\n+38111 38112 38113 38114 38115 38116 38117 38118 38119 38120 38121 38122 38123 38124 38125\n+38126 38127 38128 38129 38130 38131 38132 38133 38134 38135 38136 38137 38138 38139 38140\n+38141 38142 38143 38144 38145 38146 38147 38148 38149 38150 38151 38152 38153 38154 38155\n+38156 38157 38158 38159 38160 38161 38162 38163 38164 38165 38166 38167 38168 38169 38170\n+38171 38172 38173 38174 38175 38176 38177 38178 38179 38180 38181 38182 38183 38184 38185\n+38186 38187 38188 38189 38190 38191 38192 38193 38194 38195 38196 38197 38198 38199 38200\n+38201 38202 38203 38204 38205 38206 38207 38208 38209 38210 38211 38212 38213 38214 38215\n+38216 38217 38218 38219 38220 38221 38222 38223 38224 38225 38226 38227 38228 38229 38230\n+38231 38232 38233 38234 38235 38236 38237 38238 38239 38240 38241 38242 38243 38244 38245\n+38246 38247 38248 38249 38250 38251 38252 38253 38254 38255 38256 38257 38258 38259 38260\n+38261 38262 38263 38264 38265 38266 38267 38268 38269 38270 38271 38272 38273 38274 38275\n+38276 38277 38278 38279 38280 38281 38282 38283 38284 38285 38286 38287 38288 38289 38290\n+38291 38292 38293 38294 38295 38296 38297 38298 38299 38300 38301 38302 38303 38304 38305\n+38306 38307 38308 38309 38310 38311 38312 38313 38314 38315 38316 38317 38318 38319 38320\n+38321 38322 38323 38324 38325 38326 38327 38328 38329 38330 38331 38332 38333 38334 38335\n+38336 38337 38338 38339 38340 38341 38342 38343 38344 38345 38346 38347 38348 38349 38350\n+38351 38352 38353 38354 38355 38356 38357 38358 38359 38360 38361 38362 38363 38364 38365\n+38366 38367 38368 38369 38370 38371 38372 38373 38374 38375 38376\n+[ !Protein_&_non-Water ]\n+38369 38370 38371 38372 38373 38374 38375 38376\n' |
| b |
| diff -r ec3f665cca3e -r 5642f48f5698 test-data/md_0_1.xvg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/md_0_1.xvg Wed Nov 20 11:13:22 2019 -0500 |
| b |
| @@ -0,0 +1,37 @@ +# This file was created Sat Nov 9 15:20:20 2019 +# Created by: +# :-) GROMACS - gmx energy, 2019.1 (-: +# +# Executable: /home/simon/miniconda3/envs/gmx/bin/gmx +# Data prefix: /home/simon/miniconda3/envs/gmx +# Working dir: /home/simon/Repos/galaxy-tools-compchem/tools/gromacs +# Command line: +# gmx energy -f test-data/md_0_1.edr -o xvg5.xvg +# gmx energy is part of G R O M A C S: +# +# Gromacs Runs One Microsecond At Cannonball Speeds +# +@ title "GROMACS Energies" +@ xaxis label "Time (ps)" +@ yaxis label "(kJ/mol), (K)" +@TYPE xy +@ view 0.15, 0.15, 0.75, 0.85 +@ legend on +@ legend box on +@ legend loctype view +@ legend 0.78, 0.8 +@ legend length 2 +@ s0 legend "Potential" +@ s1 legend "Total Energy" +@ s2 legend "Temperature" + 0.000000 -593300.312500 -497358.281250 300.761719 + 0.100000 -592522.125000 -497450.843750 298.032074 + 0.200000 -593496.500000 -497942.718750 299.544647 + 0.300000 -593921.062500 -497878.187500 301.077850 + 0.400000 -593262.062500 -497926.406250 298.860870 + 0.500000 -593674.437500 -498809.312500 297.385773 + 0.600000 -594222.062500 -498825.562500 299.051605 + 0.700000 -593496.625000 -498020.125000 299.302399 + 0.800000 -593813.875000 -498131.031250 299.949219 + 0.900000 -594351.437500 -498515.812500 300.428131 + 1.000000 -595232.000000 -499672.000000 299.564087 |
| b |
| diff -r ec3f665cca3e -r 5642f48f5698 test-data/posre_cl.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posre_cl.itp Wed Nov 20 11:13:22 2019 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +; position restraints for CL of LYSOZYME in water + +[ position_restraints ] +; i funct fcx fcy fcz +38369 1 500 600 700 +38370 1 500 600 700 +38371 1 500 600 700 +38372 1 500 600 700 +38373 1 500 600 700 +38374 1 500 600 700 +38375 1 500 600 700 +38376 1 500 600 700 |