| Previous changeset 5:35b314fe6c90 (2019-10-30) Next changeset 7:cf03bccaa325 (2019-12-01) |
|
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" |
|
modified:
macros.xml setup.xml |
|
added:
test-data/md_0_1.ndx test-data/md_0_1.xvg test-data/posre_cl.itp |
| b |
| diff -r 35b314fe6c90 -r c7bcae9fe040 macros.xml --- a/macros.xml Wed Oct 30 13:35:25 2019 -0400 +++ b/macros.xml Wed Nov 20 11:16:14 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 35b314fe6c90 -r c7bcae9fe040 setup.xml --- a/setup.xml Wed Oct 30 13:35:25 2019 -0400 +++ b/setup.xml Wed Nov 20 11:16:14 2019 -0500 |
| [ |
| @@ -9,13 +9,11 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '$pdb_input' ./pdb_input.pdb && - gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh &>> verbose.txt && - gmx editconf -f processed.gro -o newbox.gro -c -d $box_d -bt $box_type &>> verbose.txt + gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh -merge all &>> verbose.txt ]]></command> <inputs> - <!-- PDB2GMX VARS --> <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/> <param argument="water" type="select" label="Water model" help="Model for simulating water molecules in the solvent"> <option value="tip3p" selected="true">TIP3P</option> @@ -46,27 +44,15 @@ </param> <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." /> - - <!-- EDITCONF VARS --> - <param argument="box_d" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="10.0" help="Dimensions of the box in which simulation will take place" /> - <param argument="box_type" type="select" label="Box type" - help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times."> - <option value="cubic">Rectangular box with all sides equal</option> - <option value="triclinic">Triclinic</option> - <option value="dodecahedron">represents a rhombic dodecahedron</option> - <option value="octahedron">truncated octahedron</option> - </param> - <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> + <expand macro="log" /> </inputs> <outputs> <data name="output1" format="top" from_work_dir="topol.top"/> - <data name="output2" format="gro" from_work_dir="newbox.gro"/> + <data name="output2" format="gro" from_work_dir="processed.gro"/> <data name="output3" format="itp" from_work_dir="posres.itp"/> - <data name="report" format="txt" from_work_dir="verbose.txt"> - <filter>capture_log</filter> - </data> + <expand macro="log_outputs" /> </outputs> <tests> <test> @@ -77,7 +63,7 @@ <param name="box_d" value="1.0" /> <param name="box_type" value="cubic" /> <output name="output1" file="topol.top" ftype="top" compare="diff" lines_diff="20"/> - <output name="output2" file="newbox.gro" ftype="gro"/> + <output name="output2" file="processed.gro" ftype="gro"/> <output name="output3" file="posres.itp" ftype="itp"/> </test> </tests> @@ -87,7 +73,7 @@ **What it does** -This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command and also defining a simulation box with editconf. +This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command. Please note that the tool will only successfully generate a topology for residues it recognizes (i.e. standard amino acids). If the structure contains other components such as ligands, these should be separately parameterized with the AmberTools or ACPYPE tools. In this case, make sure to also use an AMBER forcefield for this tool to ensure compatability with the ligand topology. @@ -99,7 +85,6 @@ - PDB file. - Water model and forcefield must be specified. - - Parameters for the simulation box (dimensions and shape). _____ |
| b |
| diff -r 35b314fe6c90 -r c7bcae9fe040 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 11:16:14 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 35b314fe6c90 -r c7bcae9fe040 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 11:16:14 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 35b314fe6c90 -r c7bcae9fe040 test-data/posre_cl.itp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/posre_cl.itp Wed Nov 20 11:16:14 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 |