Mercurial > repos > metexplore > met4j
comparison tools/convert/Tab2Sbml/Tab2Sbml.xml @ 9:0976a6257300 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
| author | metexplore |
|---|---|
| date | Fri, 31 Jan 2025 18:28:53 +0000 |
| parents | 7a6f2380fc1d |
| children | 6a112eaf8f38 |
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| 8:1274e2a62479 | 9:0976a6257300 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
| 2 <tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="MET4J_VERSION_TEST"> | 2 <tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="develop"> |
| 3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> | 3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> |
| 4 <xrefs> | 4 <xrefs> |
| 5 <xref type="bio.tools">met4j</xref> | 5 <xref type="bio.tools">met4j</xref> |
| 6 </xrefs> | 6 </xrefs> |
| 7 <requirements> | 7 <requirements> |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': |
| 11 -ci "$colid" | 11 -ci "$colid" |
| 12 #end if | 12 #end if |
| 13 #if str($colformula) != 'nan': | 13 #if str($colformula) != 'nan': |
| 17 $mp | 17 $mp |
| 18 #if str($e): | 18 #if str($e): |
| 19 -e "$e" | 19 -e "$e" |
| 20 #end if | 20 #end if |
| 21 #if str($i): | 21 #if str($i): |
| 22 -i "$i" | 22 -irr "$i" |
| 23 #end if | 23 #end if |
| 24 #if str($r): | 24 #if str($r): |
| 25 -r "$r" | 25 -rev "$r" |
| 26 #end if | 26 #end if |
| 27 -in "$in" | 27 -i "$in" |
| 28 #if str($id): | 28 #if str($id): |
| 29 -id "$id" | 29 -id "$id" |
| 30 #end if | 30 #end if |
| 31 $createCompartment | 31 $createCompartment |
| 32 #if str($defaultCompartment): | 32 #if str($defaultCompartment): |
| 33 -dcpt "$defaultCompartment" | 33 -dcpt "$defaultCompartment" |
| 34 #end if | 34 #end if |
| 35 #if str($nSkip) != 'nan': | 35 #if str($nSkip) != 'nan': |
| 36 -n "$nSkip" | 36 -n "$nSkip" |
| 37 #end if | 37 #end if |
| 38 -sbml "$sbml" | 38 -o "$sbml" |
| 39 ]]></command> | 39 ]]></command> |
| 40 <inputs> | 40 <inputs> |
| 41 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> | 41 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/> |
| 42 <param argument="-cf" label="[2] number of the column where are the reaction formulas" name="colformula" optional="true" type="integer" value="2"/> | 42 <param argument="-cf" label="[2] number of the column where are the reaction formulas" name="colformula" optional="true" type="integer" value="2"/> |
| 43 <param argument="-rp" checked="false" falsevalue="" label="[deactivated] format the reaction ids in a Palsson way (R_***)" name="rp" truevalue="-rp" type="boolean" value="false"/> | 43 <param argument="-rp" checked="false" falsevalue="" label="[deactivated] format the reaction ids in a Palsson way (R_***)" name="rp" truevalue="-rp" type="boolean" value="false"/> |
| 45 <param argument="-e" label="[_b] flag to assign metabolite as external" name="e" optional="true" type="text" value="_b"> | 45 <param argument="-e" label="[_b] flag to assign metabolite as external" name="e" optional="true" type="text" value="_b"> |
| 46 <sanitizer invalid_char="_"> | 46 <sanitizer invalid_char="_"> |
| 47 <valid initial="string.printable"/> | 47 <valid initial="string.printable"/> |
| 48 </sanitizer> | 48 </sanitizer> |
| 49 </param> | 49 </param> |
| 50 <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> | 50 <param argument="-irr" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> |
| 51 <sanitizer invalid_char="_"> | 51 <sanitizer invalid_char="_"> |
| 52 <valid initial="string.printable"/> | 52 <valid initial="string.printable"/> |
| 53 </sanitizer> | 53 </sanitizer> |
| 54 </param> | 54 </param> |
| 55 <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> | 55 <param argument="-rev" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> |
| 56 <sanitizer invalid_char="_"> | 56 <sanitizer invalid_char="_"> |
| 57 <valid initial="string.printable"/> | 57 <valid initial="string.printable"/> |
| 58 </sanitizer> | 58 </sanitizer> |
| 59 </param> | 59 </param> |
| 60 <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/> | 60 <param argument="-i" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/> |
| 61 <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA"> | 61 <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA"> |
| 62 <sanitizer invalid_char="_"> | 62 <sanitizer invalid_char="_"> |
| 63 <valid initial="string.printable"/> | 63 <valid initial="string.printable"/> |
| 64 </sanitizer> | 64 </sanitizer> |
| 65 </param> | 65 </param> |
| 74 <outputs> | 74 <outputs> |
| 75 <data format="sbml" name="sbml"/> | 75 <data format="sbml" name="sbml"/> |
| 76 </outputs> | 76 </outputs> |
| 77 <tests> | 77 <tests> |
| 78 <test> | 78 <test> |
| 79 | |
| 80 | |
| 81 | |
| 82 | |
| 83 | |
| 84 | |
| 85 | |
| 86 | |
| 87 | |
| 88 | |
| 89 | |
| 79 <param name="in" value="toy_model.tsv"/> | 90 <param name="in" value="toy_model.tsv"/> |
| 91 | |
| 92 | |
| 93 | |
| 94 | |
| 95 | |
| 96 | |
| 97 | |
| 98 | |
| 99 | |
| 100 | |
| 101 | |
| 80 <output ftype="sbml" name="sbml"> | 102 <output ftype="sbml" name="sbml"> |
| 103 | |
| 104 | |
| 105 | |
| 106 | |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 | |
| 112 | |
| 113 | |
| 81 <assert_contents> | 114 <assert_contents> |
| 115 | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 | |
| 121 | |
| 122 | |
| 123 | |
| 124 | |
| 125 | |
| 82 <is_valid_xml/> | 126 <is_valid_xml/> |
| 127 | |
| 128 | |
| 129 | |
| 130 | |
| 131 | |
| 132 | |
| 133 | |
| 134 | |
| 135 | |
| 136 | |
| 137 | |
| 83 <has_line_matching expression=".*reaction .*" n="7"/> | 138 <has_line_matching expression=".*reaction .*" n="7"/> |
| 139 | |
| 140 | |
| 141 | |
| 142 | |
| 143 | |
| 144 | |
| 145 | |
| 146 | |
| 147 | |
| 148 | |
| 149 | |
| 84 <has_line_matching expression=".*species .*" n="8"/> | 150 <has_line_matching expression=".*species .*" n="8"/> |
| 151 | |
| 152 | |
| 153 | |
| 154 | |
| 155 | |
| 156 | |
| 157 | |
| 158 | |
| 159 | |
| 160 | |
| 161 | |
| 85 </assert_contents> | 162 </assert_contents> |
| 163 | |
| 164 | |
| 165 | |
| 166 | |
| 167 | |
| 168 | |
| 169 | |
| 170 | |
| 171 | |
| 172 | |
| 173 | |
| 86 </output> | 174 </output> |
| 175 | |
| 176 | |
| 177 | |
| 178 | |
| 179 | |
| 180 | |
| 181 | |
| 182 | |
| 183 | |
| 184 | |
| 185 | |
| 87 </test> | 186 </test> |
| 88 <test> | 187 <test> |
| 188 | |
| 189 | |
| 190 | |
| 191 | |
| 192 | |
| 193 | |
| 194 | |
| 195 | |
| 196 | |
| 197 | |
| 198 | |
| 89 <param name="in" value="toy_model_otherColumns.tsv"/> | 199 <param name="in" value="toy_model_otherColumns.tsv"/> |
| 200 | |
| 201 | |
| 202 | |
| 203 | |
| 204 | |
| 205 | |
| 206 | |
| 207 | |
| 208 | |
| 209 | |
| 210 | |
| 90 <param name="colid" value="2"/> | 211 <param name="colid" value="2"/> |
| 212 | |
| 213 | |
| 214 | |
| 215 | |
| 216 | |
| 217 | |
| 218 | |
| 219 | |
| 220 | |
| 221 | |
| 222 | |
| 91 <param name="colformula" value="3"/> | 223 <param name="colformula" value="3"/> |
| 224 | |
| 225 | |
| 226 | |
| 227 | |
| 228 | |
| 229 | |
| 230 | |
| 231 | |
| 232 | |
| 233 | |
| 234 | |
| 92 <output ftype="sbml" name="sbml"> | 235 <output ftype="sbml" name="sbml"> |
| 236 | |
| 237 | |
| 238 | |
| 239 | |
| 240 | |
| 241 | |
| 242 | |
| 243 | |
| 244 | |
| 245 | |
| 246 | |
| 93 <assert_contents> | 247 <assert_contents> |
| 248 | |
| 249 | |
| 250 | |
| 251 | |
| 252 | |
| 253 | |
| 254 | |
| 255 | |
| 256 | |
| 257 | |
| 258 | |
| 94 <is_valid_xml/> | 259 <is_valid_xml/> |
| 260 | |
| 261 | |
| 262 | |
| 263 | |
| 264 | |
| 265 | |
| 266 | |
| 267 | |
| 268 | |
| 269 | |
| 270 | |
| 95 <has_line_matching expression=".*reaction .*" n="7"/> | 271 <has_line_matching expression=".*reaction .*" n="7"/> |
| 272 | |
| 273 | |
| 274 | |
| 275 | |
| 276 | |
| 277 | |
| 278 | |
| 279 | |
| 280 | |
| 281 | |
| 282 | |
| 96 <has_line_matching expression=".*species .*" n="8"/> | 283 <has_line_matching expression=".*species .*" n="8"/> |
| 284 | |
| 285 | |
| 286 | |
| 287 | |
| 288 | |
| 289 | |
| 290 | |
| 291 | |
| 292 | |
| 293 | |
| 294 | |
| 97 </assert_contents> | 295 </assert_contents> |
| 296 | |
| 297 | |
| 298 | |
| 299 | |
| 300 | |
| 301 | |
| 302 | |
| 303 | |
| 304 | |
| 305 | |
| 306 | |
| 98 </output> | 307 </output> |
| 308 | |
| 309 | |
| 310 | |
| 311 | |
| 312 | |
| 313 | |
| 314 | |
| 315 | |
| 316 | |
| 317 | |
| 318 | |
| 99 </test> | 319 </test> |
| 100 <test> | 320 <test> |
| 321 | |
| 322 | |
| 323 | |
| 324 | |
| 325 | |
| 326 | |
| 327 | |
| 328 | |
| 329 | |
| 330 | |
| 331 | |
| 101 <param name="in" value="toy_model_otherSigns.tsv"/> | 332 <param name="in" value="toy_model_otherSigns.tsv"/> |
| 333 | |
| 334 | |
| 335 | |
| 336 | |
| 337 | |
| 338 | |
| 339 | |
| 340 | |
| 341 | |
| 342 | |
| 343 | |
| 102 <param name="i" value="->"/> | 344 <param name="i" value="->"/> |
| 345 | |
| 346 | |
| 347 | |
| 348 | |
| 349 | |
| 350 | |
| 351 | |
| 352 | |
| 353 | |
| 354 | |
| 355 | |
| 103 <param name="r" value="="/> | 356 <param name="r" value="="/> |
| 357 | |
| 358 | |
| 359 | |
| 360 | |
| 361 | |
| 362 | |
| 363 | |
| 364 | |
| 365 | |
| 366 | |
| 367 | |
| 104 <output ftype="sbml" name="sbml"> | 368 <output ftype="sbml" name="sbml"> |
| 369 | |
| 370 | |
| 371 | |
| 372 | |
| 373 | |
| 374 | |
| 375 | |
| 376 | |
| 377 | |
| 378 | |
| 379 | |
| 105 <assert_contents> | 380 <assert_contents> |
| 381 | |
| 382 | |
| 383 | |
| 384 | |
| 385 | |
| 386 | |
| 387 | |
| 388 | |
| 389 | |
| 390 | |
| 391 | |
| 106 <is_valid_xml/> | 392 <is_valid_xml/> |
| 393 | |
| 394 | |
| 395 | |
| 396 | |
| 397 | |
| 398 | |
| 399 | |
| 400 | |
| 401 | |
| 402 | |
| 403 | |
| 107 <has_line_matching expression=".*reaction .*" n="7"/> | 404 <has_line_matching expression=".*reaction .*" n="7"/> |
| 405 | |
| 406 | |
| 407 | |
| 408 | |
| 409 | |
| 410 | |
| 411 | |
| 412 | |
| 413 | |
| 414 | |
| 415 | |
| 108 <has_line_matching expression=".*species .*" n="8"/> | 416 <has_line_matching expression=".*species .*" n="8"/> |
| 417 | |
| 418 | |
| 419 | |
| 420 | |
| 421 | |
| 422 | |
| 423 | |
| 424 | |
| 425 | |
| 426 | |
| 427 | |
| 109 </assert_contents> | 428 </assert_contents> |
| 429 | |
| 430 | |
| 431 | |
| 432 | |
| 433 | |
| 434 | |
| 435 | |
| 436 | |
| 437 | |
| 438 | |
| 439 | |
| 110 </output> | 440 </output> |
| 441 | |
| 442 | |
| 443 | |
| 444 | |
| 445 | |
| 446 | |
| 447 | |
| 448 | |
| 449 | |
| 450 | |
| 451 | |
| 111 </test> | 452 </test> |
| 112 <test> | 453 <test> |
| 454 | |
| 455 | |
| 456 | |
| 457 | |
| 458 | |
| 459 | |
| 460 | |
| 461 | |
| 462 | |
| 463 | |
| 464 | |
| 113 <param name="in" value="toy_model.tsv"/> | 465 <param name="in" value="toy_model.tsv"/> |
| 466 | |
| 467 | |
| 468 | |
| 469 | |
| 470 | |
| 471 | |
| 472 | |
| 473 | |
| 474 | |
| 475 | |
| 476 | |
| 114 <param name="rp" value="true"/> | 477 <param name="rp" value="true"/> |
| 478 | |
| 479 | |
| 480 | |
| 481 | |
| 482 | |
| 483 | |
| 484 | |
| 485 | |
| 486 | |
| 487 | |
| 488 | |
| 115 <param name="mp" value="true"/> | 489 <param name="mp" value="true"/> |
| 490 | |
| 491 | |
| 492 | |
| 493 | |
| 494 | |
| 495 | |
| 496 | |
| 497 | |
| 498 | |
| 499 | |
| 500 | |
| 116 <param name="e" value="_e"/> | 501 <param name="e" value="_e"/> |
| 502 | |
| 503 | |
| 504 | |
| 505 | |
| 506 | |
| 507 | |
| 508 | |
| 509 | |
| 510 | |
| 511 | |
| 512 | |
| 117 <param name="createCompartment" value="true"/> | 513 <param name="createCompartment" value="true"/> |
| 514 | |
| 515 | |
| 516 | |
| 517 | |
| 518 | |
| 519 | |
| 520 | |
| 521 | |
| 522 | |
| 523 | |
| 524 | |
| 118 <output ftype="sbml" name="sbml"> | 525 <output ftype="sbml" name="sbml"> |
| 526 | |
| 527 | |
| 528 | |
| 529 | |
| 530 | |
| 531 | |
| 532 | |
| 533 | |
| 534 | |
| 535 | |
| 536 | |
| 119 <assert_contents> | 537 <assert_contents> |
| 538 | |
| 539 | |
| 540 | |
| 541 | |
| 542 | |
| 543 | |
| 544 | |
| 545 | |
| 546 | |
| 547 | |
| 548 | |
| 120 <is_valid_xml/> | 549 <is_valid_xml/> |
| 550 | |
| 551 | |
| 552 | |
| 553 | |
| 554 | |
| 555 | |
| 556 | |
| 557 | |
| 558 | |
| 559 | |
| 560 | |
| 121 <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> | 561 <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> |
| 562 | |
| 563 | |
| 564 | |
| 565 | |
| 566 | |
| 567 | |
| 568 | |
| 569 | |
| 570 | |
| 571 | |
| 572 | |
| 122 <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> | 573 <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> |
| 574 | |
| 575 | |
| 576 | |
| 577 | |
| 578 | |
| 579 | |
| 580 | |
| 581 | |
| 582 | |
| 583 | |
| 584 | |
| 123 <has_line_matching expression=".*id=.R_reac2.*" n="1"/> | 585 <has_line_matching expression=".*id=.R_reac2.*" n="1"/> |
| 586 | |
| 587 | |
| 588 | |
| 589 | |
| 590 | |
| 591 | |
| 592 | |
| 593 | |
| 594 | |
| 595 | |
| 596 | |
| 124 </assert_contents> | 597 </assert_contents> |
| 598 | |
| 599 | |
| 600 | |
| 601 | |
| 602 | |
| 603 | |
| 604 | |
| 605 | |
| 606 | |
| 607 | |
| 608 | |
| 125 </output> | 609 </output> |
| 610 | |
| 611 | |
| 612 | |
| 613 | |
| 614 | |
| 615 | |
| 616 | |
| 617 | |
| 618 | |
| 619 | |
| 620 | |
| 126 </test> | 621 </test> |
| 127 <test> | 622 <test> |
| 623 | |
| 624 | |
| 625 | |
| 626 | |
| 627 | |
| 628 | |
| 629 | |
| 630 | |
| 631 | |
| 632 | |
| 633 | |
| 128 <param name="in" value="toy_model.tsv"/> | 634 <param name="in" value="toy_model.tsv"/> |
| 635 | |
| 636 | |
| 637 | |
| 638 | |
| 639 | |
| 640 | |
| 641 | |
| 642 | |
| 643 | |
| 644 | |
| 645 | |
| 129 <param name="id" value="myModel"/> | 646 <param name="id" value="myModel"/> |
| 647 | |
| 648 | |
| 649 | |
| 650 | |
| 651 | |
| 652 | |
| 653 | |
| 654 | |
| 655 | |
| 656 | |
| 657 | |
| 130 <output ftype="sbml" name="sbml"> | 658 <output ftype="sbml" name="sbml"> |
| 659 | |
| 660 | |
| 661 | |
| 662 | |
| 663 | |
| 664 | |
| 665 | |
| 666 | |
| 667 | |
| 668 | |
| 669 | |
| 131 <assert_contents> | 670 <assert_contents> |
| 671 | |
| 672 | |
| 673 | |
| 674 | |
| 675 | |
| 676 | |
| 677 | |
| 678 | |
| 679 | |
| 680 | |
| 681 | |
| 132 <is_valid_xml/> | 682 <is_valid_xml/> |
| 683 | |
| 684 | |
| 685 | |
| 686 | |
| 687 | |
| 688 | |
| 689 | |
| 690 | |
| 691 | |
| 692 | |
| 693 | |
| 133 <has_line_matching expression=".*myModel.*" n="1"/> | 694 <has_line_matching expression=".*myModel.*" n="1"/> |
| 695 | |
| 696 | |
| 697 | |
| 698 | |
| 699 | |
| 700 | |
| 701 | |
| 702 | |
| 703 | |
| 704 | |
| 705 | |
| 134 </assert_contents> | 706 </assert_contents> |
| 707 | |
| 708 | |
| 709 | |
| 710 | |
| 711 | |
| 712 | |
| 713 | |
| 714 | |
| 715 | |
| 716 | |
| 717 | |
| 135 </output> | 718 </output> |
| 719 | |
| 720 | |
| 721 | |
| 722 | |
| 723 | |
| 724 | |
| 725 | |
| 726 | |
| 727 | |
| 728 | |
| 729 | |
| 136 </test> | 730 </test> |
| 137 </tests> | 731 </tests> |
| 138 <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help> | 732 <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help> |
| 139 <citations/> | 733 <citations/> |
| 140 </tool> | 734 </tool> |