Mercurial > repos > pieterlukasse > nist_wrapper
annotate nist_wrapper.xml @ 13:251e23773999
adding code to ignore wine stderr ouptut
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 23 Jan 2015 12:34:33 +0100 |
| parents | a62374fcee9c |
| children | 92cf554fca03 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="nist_wrapper" name="NIST MSSEARCH" version="0.0.1"> |
| 2 <!-- | |
| 3 This part is a WORKAROUND for the wine X11 dependency, allowing it to run headless : | |
| 4 -> install Xvfb and enable it on a port, say 995: | |
| 5 -> make sure this gets executed: export DISPLAY=:995; | |
| 6 --> | |
| 7 <description> Runs NIST's msseach program to match spectra against metabolite libraries</description> | |
| 2 | 8 |
| 9 <requirements> | |
| 10 <requirement name="package" version="0.2">nist_wrapper_venv</requirement> | |
| 11 </requirements> | |
| 12 | |
| 11 | 13 <command interpreter="export DISPLAY=:995; python"> |
| 0 | 14 nist_wrapper.py |
| 4 | 15 "/home/galaxy/.wine/drive_c/NIST" |
| 0 | 16 $nistIniFile |
| 17 $spectraFile | |
| 18 $outputFile | |
| 3 | 19 $outputFileFinal |
| 7 | 20 $outputLog |
| 3 | 21 $htmlReportFile |
| 22 $htmlReportFile.files_path | |
| 0 | 23 </command> |
| 24 <inputs> | |
| 25 <param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/> | |
| 26 | |
| 27 <param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum" | |
| 28 help="Top X matches for each spectrum will be written to output file." /> | |
| 29 | |
| 30 </inputs> | |
| 31 <configfiles> | |
| 32 | |
| 33 <configfile name="nistIniFile">[MAIN] | |
| 34 Version=2.0 | |
| 35 Library Directory=C:\NISTDEMO\MSSEARCH\ | |
| 36 Program=NIST MS | |
| 37 Active Frame=0 | |
| 38 Placement_flags=2 | |
| 39 Placement_show=3 | |
| 40 Placement_minx=-32000 | |
| 41 Placement_miny=-32000 | |
| 42 Placement_maxx=-1 | |
| 43 Placement_maxy=-1 | |
| 44 Placement_left=0 | |
| 45 Placement_top=84 | |
| 46 Placement_right=1440 | |
| 47 Placement_bottom=827 | |
| 48 Wrong Libraries= | |
| 49 Active Show=3 | |
| 50 Display Warning=1 | |
| 51 Display Info=0 | |
| 52 [Search Options] | |
| 53 Automatic=1 | |
| 54 Type=1 | |
| 55 As MW=1 | |
| 56 MW=1 | |
| 57 Reverse=0 | |
| 58 Penalize=0 | |
| 59 Search with MW=1 | |
| 60 Preasearch=0 | |
| 61 Apply Limits=0 | |
| 62 Min Mass Type=0 | |
| 63 Min Mass=1 | |
| 64 Max Mass ON=0 | |
| 65 Max Mass=2000 | |
| 66 Min Abund ON=0 | |
| 67 Min Abund=1 | |
| 68 Printing=0 | |
| 69 Return Focus=0 | |
| 70 Hits to Print=${hitsToReport} | |
| 71 Print Spectra=1 | |
| 72 Print Structure=1 | |
| 73 Apply MaxLength=0 | |
| 74 MaxLength=2000 | |
| 75 Sort Mode=0 | |
| 76 Match Clusters=1 | |
| 77 Match Rings=1 | |
| 78 Weighting=0 | |
| 79 Use Specified Parent=0 | |
| 80 Ignore Precursor=0 | |
| 81 Parent Mass=0 | |
| 82 Precursor Tolerance=1.6 | |
| 83 Ions Tolerance=0.8 | |
| 84 [Libraries] | |
| 85 Library_0=mainlib | |
| 86 Library_1= | |
| 87 Library_2= | |
| 88 Library_3= | |
| 89 Library_4= | |
| 90 Library_5= | |
| 91 Library_6= | |
| 92 Library_7= | |
| 93 Library_8= | |
| 94 Library_9= | |
| 95 Library_10= | |
| 96 Library_11= | |
| 97 Library_12= | |
| 98 Library_13= | |
| 99 Library_14= | |
| 100 Library_15= | |
| 101 Order_0=1 1 | |
| 102 Order_1=1 1 | |
| 103 Order_2=1 1 | |
| 104 Order_3=1 1 | |
| 105 Order_4=1 1 | |
| 106 Order_5=1 1 | |
| 107 Order_6=1 1 | |
| 108 Order_7=1 1 | |
| 109 Order_8=1 1 | |
| 110 Order_9=1 1 | |
| 111 [ICHI] | |
| 112 On=1 | |
| 113 Isotope=1 | |
| 114 Stereo=0 | |
| 115 Derivative=1 | |
| 116 [Import] | |
| 117 Dir=C:\NISTDEMO\MSSEARCH\ | |
| 118 Synonyms=1 | |
| 119 Filter=1 | |
| 120 Coeff=1 0 | |
| 121 [Structure Import] | |
| 122 Dir=C:\NISTDEMO\MSSEARCH\ | |
| 123 Filter=1 | |
| 124 [Export] | |
| 125 Dir=C:\NISTDEMO\MSSEARCH\ | |
| 126 Synonyms=1 | |
| 127 Filter=1 | |
| 128 Coeff=1 0 | |
| 129 [Search Options] | |
| 130 Automatic=1 | |
| 131 [Library Search] | |
| 132 SpecList Tab=1 | |
| 133 Placement_flags=2 | |
| 134 Placement_show=3 | |
| 135 ;Layout=1 | |
| 136 ;Hit Splitter Orientation=1 | |
| 137 ;List Tab=0 | |
| 138 ;Compare Tab=0 | |
| 139 ;Hit Tab=0 | |
| 140 ;Unknown Tab=0 | |
| 141 Placement_minx=-1 | |
| 142 Placement_miny=-1 | |
| 143 ;Placement_maxx=-4 | |
| 144 Placement_maxx=-8 | |
| 145 ;Placement_maxy=-23 | |
| 146 Placement_maxy=-30 | |
| 147 Placement_left=0 | |
| 148 Placement_top=1 | |
| 149 Placement_right=678 | |
| 150 Placement_bottom=397 | |
| 151 Splitter=0.314139 | |
| 152 List Splitter=0 0 | |
| 153 Unknown Splitter=0.493119 | |
| 154 Unknown Splitter Orientation=1 | |
| 155 ;Compare Splitter=0.3333 0.3333 | |
| 156 Compare Splitter=0 0 | |
| 157 Hit Splitter=0.493874 | |
| 158 SpecList Splitter=0.493119 | |
| 159 SpecList Splitter Orientation=1 | |
| 160 Hits Column=10 41 39 58 68 56 256 0 0 0 0 | |
| 161 ;SpecList Column=3 41 41 56 | |
| 162 ;SpecList Column=3 41 41 156 | |
| 163 SpecList Column=10 41 38 128 0 0 48 0 0 0 0 | |
| 164 Layout=1 | |
| 165 Hit Splitter Orientation=1 | |
| 166 List Tab=0 | |
| 167 Compare Tab=0 | |
| 168 Hit Tab=0 | |
| 169 Unknown Tab=0 | |
| 170 Replicates=0 | |
| 171 Exact Match=0 | |
| 172 [BAR-Summary] | |
| 173 Bars=4 | |
| 174 ScreenCX=1600 | |
| 175 ScreenCY=900 | |
| 176 [REPORT] | |
| 177 Ten Largest Peaks=1 | |
| 178 Compound Info=1 | |
| 179 Mass Intensity List=0 | |
| 180 Synonyms=1 | |
| 181 Plot=1 | |
| 182 Structure=1 | |
| 183 First Hits=1 | |
| 184 First Hits Number=3 | |
| 185 Unknown=0 | |
| 186 [Substructure Export] | |
| 187 Filter=1 | |
| 188 Dir= | |
| 189 [Substructure Import] | |
| 190 Filter=1 | |
| 191 Dir= | |
| 192 [Search AnyPeaks Options] | |
| 193 Other=0 | |
| 194 Peaks=0 | |
| 195 Hitlist size=100 | |
| 196 Peak0= | |
| 197 Peak1= | |
| 198 Peak2= | |
| 199 Peak3= | |
| 200 Peak4= | |
| 201 Peak5= | |
| 202 Peak6= | |
| 203 Peak7= | |
| 204 Peak8= | |
| 205 Peak9= | |
| 206 Peak10= | |
| 207 [Other Searches Options] | |
| 208 CAS= | |
| 209 MW=1 | |
| 210 ID= | |
| 211 EPA= | |
| 212 Formula= | |
| 213 Seq Hitlist size=100 | |
| 214 [Constraints] | |
| 215 Library ON=0 | |
| 216 Formula ON=0 | |
| 217 MW ON=0 | |
| 218 AnyPeaks ON=0 | |
| 219 Sequentiial ON=0 | |
| 220 Active MW=0 | |
| 221 MINMW=1 | |
| 222 MAXMW=2000 | |
| 223 Active Name=0 | |
| 224 Name Fragment= | |
| 225 Elements Value=0 | |
| 226 Elements Present=0 | |
| 227 Mode Elements=0 | |
| 228 Num Elements=0 | |
| 229 Elements0= | |
| 230 Elements1= | |
| 231 Elements2= | |
| 232 Elements3= | |
| 233 Elements4= | |
| 234 Elements5= | |
| 235 Elements6= | |
| 236 Elements7= | |
| 237 Elements8= | |
| 238 Elements9= | |
| 239 Num Compare Elements=0 | |
| 240 Compare Elements0= | |
| 241 Compare Elements1= | |
| 242 Compare Elements2= | |
| 243 Compare Elements3= | |
| 244 Compare Elements4= | |
| 245 Compare Elements5= | |
| 246 Compare Elements6= | |
| 247 Compare Elements7= | |
| 248 Compare Elements8= | |
| 249 Compare Elements9= | |
| 250 Active Peaks=0 | |
| 251 Mode Peaks=1 | |
| 252 Num AnyPeaks=0 | |
| 253 Active OtherDB=0 | |
| 254 OtherDB=0 | |
| 255 Active Tags=0 | |
| 256 Tags= | |
| 257 Active Peptide Sequence=0 | |
| 258 Peptide Sequence= | |
| 259 Active Proton=0 | |
| 260 Proton Mode=0 | |
| 261 Proton Low= | |
| 262 Proton Hi= | |
| 263 Proton Exact= | |
| 264 Active Charge=0 | |
| 265 Charge Mode=0 | |
| 266 Charge Low= | |
| 267 Charge Hi= | |
| 268 Charge Exact= | |
| 269 Active Residue=0 | |
| 270 Residue Mode=0 | |
| 271 Residue Low= | |
| 272 Residue Hi= | |
| 273 Residue Exact= | |
| 274 [Peptide Search Options] | |
| 275 Cysteine Modification=0 | |
| 276 Comment Fields= | |
| 277 Show Fields On Plot=1 | |
| 278 TF qry=0 | |
| 279 E Omssa=0 | |
| 280 TF lib=0 | |
| 281 RevImp=0 | |
| 282 Weight Omssa=0 | |
| 283 Weight Num Rep=0 | |
| 284 Weight Qtof=0 | |
| 285 Treshold=0 | |
| 286 [Library Hit] | |
| 287 Font Name=MS Shell Dlg | |
| 288 Font Pts=-8 | |
| 289 Font Width=0 | |
| 290 Font Esc=0 | |
| 291 Font Orientation=0 | |
| 292 Font Weight=400 | |
| 293 Font IUSC=0 | |
| 294 Font PCQP=654311424 | |
| 295 Color=0 255 16711680 16777215 16777215 0 | |
| 296 Order Number=1 | |
| 297 Structure Only=0 | |
| 298 Library=0 | |
| 299 Structure Size=50 | |
| 300 Match=1 | |
| 301 Probability=1 | |
| 302 Reverse Match=1 | |
| 303 Clear History=0 | |
| 304 [Library Spec List] | |
| 305 Font Name=MS Shell Dlg | |
| 306 Font Pts=-8 | |
| 307 Font Width=0 | |
| 308 Font Esc=0 | |
| 309 Font Orientation=0 | |
| 310 Font Weight=400 | |
| 311 Font IUSC=0 | |
| 312 Font PCQP=654311424 | |
| 313 Color=0 255 16711680 16777215 16777215 0 | |
| 314 Order Number=1 | |
| 315 Structure Only=0 | |
| 316 Library=0 | |
| 317 Structure Size=50 | |
| 318 Match=0 | |
| 319 Probability=0 | |
| 320 Reverse Match=0 | |
| 321 Clear History=0 | |
| 322 [Library Unknown Plot] | |
| 323 Font Name=MS Shell Dlg | |
| 324 Font Pts=-8 | |
| 325 Font Width=0 | |
| 326 Font Esc=0 | |
| 327 Font Orientation=0 | |
| 328 Font Weight=400 | |
| 329 Font IUSC=0 | |
| 330 Font PCQP=654311424 | |
| 331 Color=0 255 16711680 0 255 16777215 | |
| 332 Limits ON=0 | |
| 333 Wrap=0 | |
| 334 MW=0 | |
| 335 CAS=0 | |
| 336 Formula=0 | |
| 337 Threshold=0 | |
| 338 Structure=1 | |
| 339 Width=1 | |
| 340 Mass Label=1 | |
| 341 Pep Label=0 | |
| 342 [Library Hit Plot] | |
| 343 Font Name=MS Shell Dlg | |
| 344 Font Pts=-8 | |
| 345 Font Width=0 | |
| 346 Font Esc=0 | |
| 347 Font Orientation=0 | |
| 348 Font Weight=400 | |
| 349 Font IUSC=0 | |
| 350 Font PCQP=654311424 | |
| 351 Color=0 255 16711680 0 255 16777215 | |
| 352 Limits ON=0 | |
| 353 Wrap=0 | |
| 354 MW=1 | |
| 355 CAS=0 | |
| 356 Formula=1 | |
| 357 Threshold=0 | |
| 358 Structure=1 | |
| 359 Width=1 | |
| 360 Mass Label=1 | |
| 361 Pep Label=0 | |
| 362 [Library SpecList Plot] | |
| 363 Font Name=MS Shell Dlg | |
| 364 Font Pts=-8 | |
| 365 Font Width=0 | |
| 366 Font Esc=0 | |
| 367 Font Orientation=0 | |
| 368 Font Weight=400 | |
| 369 Font IUSC=0 | |
| 370 Font PCQP=654311424 | |
| 371 Color=0 255 16711680 0 255 16777215 | |
| 372 Limits ON=0 | |
| 373 Wrap=0 | |
| 374 MW=0 | |
| 375 CAS=0 | |
| 376 Formula=0 | |
| 377 Threshold=0 | |
| 378 Structure=1 | |
| 379 Width=1 | |
| 380 Mass Label=1 | |
| 381 Pep Label=0 | |
| 382 [Library Unknown Text] | |
| 383 Font Name=MS Shell Dlg | |
| 384 Font Pts=-8 | |
| 385 Font Width=0 | |
| 386 Font Esc=0 | |
| 387 Font Orientation=0 | |
| 388 Font Weight=400 | |
| 389 Font IUSC=0 | |
| 390 Font PCQP=654311424 | |
| 391 Color=16711680 0 255 8421376 16777215 | |
| 392 Ten Peaks=1 | |
| 393 Compound=1 | |
| 394 Intensity=0 | |
| 395 Synonyms=1 | |
| 396 Rows=0 | |
| 397 Noise=0 | |
| 398 Wrap Synonyms=0 | |
| 399 RI=1 | |
| 400 RI All=1 | |
| 401 RI Num=2 | |
| 402 [Library Hit Text] | |
| 403 Font Name=MS Shell Dlg | |
| 404 Font Pts=-8 | |
| 405 Font Width=0 | |
| 406 Font Esc=0 | |
| 407 Font Orientation=0 | |
| 408 Font Weight=400 | |
| 409 Font IUSC=0 | |
| 410 Font PCQP=654311424 | |
| 411 Color=16711680 0 255 8421376 16777215 | |
| 412 Ten Peaks=1 | |
| 413 Compound=1 | |
| 414 Intensity=1 | |
| 415 Synonyms=1 | |
| 416 Rows=0 | |
| 417 Noise=0 | |
| 418 Wrap Synonyms=0 | |
| 419 RI=1 | |
| 420 RI All=1 | |
| 421 RI Num=2 | |
| 422 [Library SpecList Text] | |
| 423 Font Name=MS Shell Dlg | |
| 424 Font Pts=-8 | |
| 425 Font Width=0 | |
| 426 Font Esc=0 | |
| 427 Font Orientation=0 | |
| 428 Font Weight=400 | |
| 429 Font IUSC=0 | |
| 430 Font PCQP=654311424 | |
| 431 Color=16711680 0 255 8421376 16777215 | |
| 432 Ten Peaks=1 | |
| 433 Compound=1 | |
| 434 Intensity=0 | |
| 435 Synonyms=1 | |
| 436 Rows=0 | |
| 437 Noise=0 | |
| 438 Wrap Synonyms=0 | |
| 439 RI=1 | |
| 440 RI All=1 | |
| 441 RI Num=2 | |
| 442 [Library Compare] | |
| 443 Font Name=MS Shell Dlg | |
| 444 Font Pts=-8 | |
| 445 Font Width=0 | |
| 446 Font Esc=0 | |
| 447 Font Orientation=0 | |
| 448 Font Weight=400 | |
| 449 Font IUSC=0 | |
| 450 Font PCQP=654311424 | |
| 451 Color=0 255 16711680 32768 16777215 | |
| 452 Limit ON=0 | |
| 453 Threshold=0 | |
| 454 Show=1 | |
| 455 Show Structure=0 | |
| 456 Independent Zoom=0 | |
| 457 Width=1 | |
| 458 [Library Histogram] | |
| 459 Font Name=MS Shell Dlg | |
| 460 Font Pts=-8 | |
| 461 Font Width=0 | |
| 462 Font Esc=0 | |
| 463 Font Orientation=0 | |
| 464 Font Weight=400 | |
| 465 Font IUSC=0 | |
| 466 Font PCQP=654311424 | |
| 467 Color=0 16711680 255 16777215 | |
| 468 Discret=25 | |
| 469 Axis=1 | |
| 470 Automatic=1 | |
| 471 Min=0 | |
| 472 Max=1000 | |
| 473 [Library Display] | |
| 474 Neutral Loss=0 | |
| 475 Scale=0 | |
| 476 Min mz=0 | |
| 477 Max mz=1000 | |
| 478 Default Search Anchor=1 | |
| 479 Search Anchor=0 | |
| 480 Default Hit Anchor=1 | |
| 481 Hit Anchor=0 | |
| 482 Max Loss=70 | |
| 483 mz=10 | |
| 484 [Incremental Search] | |
| 485 Placement_flags=0 | |
| 486 Placement_show=1 | |
| 487 Placement_minx=-1 | |
| 488 Placement_miny=-1 | |
| 489 Placement_maxx=-8 | |
| 490 Placement_maxy=-30 | |
| 491 Placement_left=50 | |
| 492 Placement_top=50 | |
| 493 Placement_right=1269 | |
| 494 Placement_bottom=449 | |
| 495 Key=10METHOXYDESERPID | |
| 496 Splitter=0.333054 | |
| 497 Layout=1 | |
| 498 Plot Splitter=0.5 | |
| 499 Plot Splitter Orientation=0 | |
| 500 List Tab=0 | |
| 501 Spectrum Tab=0 | |
| 502 Alpha=0 | |
| 503 [Incremental View] | |
| 504 Font Name=MS Shell Dlg | |
| 505 Font Pts=-8 | |
| 506 Font Width=0 | |
| 507 Font Esc=0 | |
| 508 Font Orientation=0 | |
| 509 Font Weight=400 | |
| 510 Font IUSC=0 | |
| 511 Font PCQP=654311424 | |
| 512 Color=0 255 16711680 16777215 16777215 0 | |
| 513 Auto Display=1 | |
| 514 Structure Only=50 | |
| 515 [Incremental Plot] | |
| 516 Font Name=MS Shell Dlg | |
| 517 Font Pts=-8 | |
| 518 Font Width=0 | |
| 519 Font Esc=0 | |
| 520 Font Orientation=0 | |
| 521 Font Weight=400 | |
| 522 Font IUSC=0 | |
| 523 Font PCQP=654311424 | |
| 524 Color=0 255 16711680 0 255 16777215 | |
| 525 Limits ON=0 | |
| 526 Wrap=0 | |
| 527 MW=0 | |
| 528 CAS=0 | |
| 529 Formula=0 | |
| 530 Threshold=0 | |
| 531 Structure=1 | |
| 532 Width=1 | |
| 533 Mass Label=1 | |
| 534 Pep Label=0 | |
| 535 [Incremental Text] | |
| 536 Font Name=MS Shell Dlg | |
| 537 Font Pts=-8 | |
| 538 Font Width=0 | |
| 539 Font Esc=0 | |
| 540 Font Orientation=0 | |
| 541 Font Weight=400 | |
| 542 Font IUSC=0 | |
| 543 Font PCQP=654311424 | |
| 544 Color=16711680 0 255 8421376 16777215 | |
| 545 Ten Peaks=1 | |
| 546 Compound=1 | |
| 547 Intensity=0 | |
| 548 Synonyms=1 | |
| 549 Rows=0 | |
| 550 Noise=0 | |
| 551 Wrap Synonyms=0 | |
| 552 RI=1 | |
| 553 RI All=1 | |
| 554 RI Num=2 | |
| 555 [Other Search] | |
| 556 Placement_flags=0 | |
| 557 Placement_show=1 | |
| 558 Placement_minx=-1 | |
| 559 Placement_miny=-1 | |
| 560 Placement_maxx=-8 | |
| 561 Placement_maxy=-30 | |
| 562 Placement_left=25 | |
| 563 Placement_top=25 | |
| 564 Placement_right=1244 | |
| 565 Placement_bottom=424 | |
| 566 Splitter=0.332215 | |
| 567 Layout=1 | |
| 568 Plot Splitter=0.5 | |
| 569 Plot Splitter Orientation=0 | |
| 570 List Tab=0 | |
| 571 Spectrum Tab=0 | |
| 572 Replicates=0 | |
| 573 Search Mode=2 | |
| 574 Column=10 39 37 0 0 0 48 0 0 0 0 | |
| 575 [Other Hit] | |
| 576 Font Name=MS Shell Dlg | |
| 577 Font Pts=-8 | |
| 578 Font Width=0 | |
| 579 Font Esc=0 | |
| 580 Font Orientation=0 | |
| 581 Font Weight=400 | |
| 582 Font IUSC=0 | |
| 583 Font PCQP=654311424 | |
| 584 Color=0 255 16711680 16777215 16777215 0 | |
| 585 Order Number=1 | |
| 586 Structure Only=0 | |
| 587 Library=0 | |
| 588 Structure Size=50 | |
| 589 Match=0 | |
| 590 Probability=0 | |
| 591 Reverse Match=0 | |
| 592 Clear History=0 | |
| 593 [Other Plot] | |
| 594 Font Name=MS Shell Dlg | |
| 595 Font Pts=-8 | |
| 596 Font Width=0 | |
| 597 Font Esc=0 | |
| 598 Font Orientation=0 | |
| 599 Font Weight=400 | |
| 600 Font IUSC=0 | |
| 601 Font PCQP=654311424 | |
| 602 Color=0 255 16711680 0 255 16777215 | |
| 603 Limits ON=0 | |
| 604 Wrap=0 | |
| 605 MW=0 | |
| 606 CAS=0 | |
| 607 Formula=0 | |
| 608 Threshold=0 | |
| 609 Structure=1 | |
| 610 Width=1 | |
| 611 Mass Label=1 | |
| 612 Pep Label=0 | |
| 613 [Other Text] | |
| 614 Font Name=MS Shell Dlg | |
| 615 Font Pts=-8 | |
| 616 Font Width=0 | |
| 617 Font Esc=0 | |
| 618 Font Orientation=0 | |
| 619 Font Weight=400 | |
| 620 Font IUSC=0 | |
| 621 Font PCQP=654311424 | |
| 622 Color=16711680 0 255 8421376 16777215 | |
| 623 Ten Peaks=1 | |
| 624 Compound=1 | |
| 625 Intensity=0 | |
| 626 Synonyms=1 | |
| 627 Rows=0 | |
| 628 Noise=0 | |
| 629 Wrap Synonyms=0 | |
| 630 RI=1 | |
| 631 RI All=1 | |
| 632 RI Num=2 | |
| 633 [Compare] | |
| 634 Placement_flags=0 | |
| 635 Placement_show=1 | |
| 636 Placement_minx=-1 | |
| 637 Placement_miny=-1 | |
| 638 Placement_maxx=-8 | |
| 639 Placement_maxy=-30 | |
| 640 Placement_left=75 | |
| 641 Placement_top=75 | |
| 642 Placement_right=1294 | |
| 643 Placement_bottom=474 | |
| 644 Splitter=0.244898 0.244898 | |
| 645 Tab=0 | |
| 646 [Compare Plot] | |
| 647 Font Name=MS Shell Dlg | |
| 648 Font Pts=-8 | |
| 649 Font Width=0 | |
| 650 Font Esc=0 | |
| 651 Font Orientation=0 | |
| 652 Font Weight=400 | |
| 653 Font IUSC=0 | |
| 654 Font PCQP=654311424 | |
| 655 Color=0 255 16711680 0 255 16777215 | |
| 656 Limits ON=0 | |
| 657 Wrap=0 | |
| 658 MW=0 | |
| 659 CAS=0 | |
| 660 Formula=0 | |
| 661 Threshold=0 | |
| 662 Structure=1 | |
| 663 Width=1 | |
| 664 Mass Label=1 | |
| 665 Pep Label=0 | |
| 666 [Compare Result] | |
| 667 Font Name=MS Shell Dlg | |
| 668 Font Pts=-8 | |
| 669 Font Width=0 | |
| 670 Font Esc=0 | |
| 671 Font Orientation=0 | |
| 672 Font Weight=400 | |
| 673 Font IUSC=0 | |
| 674 Font PCQP=654311424 | |
| 675 Color=0 255 16711680 32768 16777215 | |
| 676 Limit ON=0 | |
| 677 Threshold=0 | |
| 678 Show=1 | |
| 679 Show Structure=0 | |
| 680 Independent Zoom=0 | |
| 681 Width=1 | |
| 682 [Compare List] | |
| 683 Font Name=MS Shell Dlg | |
| 684 Font Pts=-8 | |
| 685 Font Width=0 | |
| 686 Font Esc=0 | |
| 687 Font Orientation=0 | |
| 688 Font Weight=400 | |
| 689 Font IUSC=0 | |
| 690 Font PCQP=654311424 | |
| 691 Color=32768 0 255 16711680 16777215 0 255 | |
| 692 Names=1 | |
| 693 No Structure=0 | |
| 694 Limits ON=0 | |
| 695 Threshold=0 | |
| 696 Spectra on Page=3 | |
| 697 Overwrite=1 | |
| 698 Insert=1 | |
| 699 Hits=3 | |
| 700 Wrap=0 | |
| 701 MW=0 | |
| 702 CAS=0 | |
| 703 Formula=0 | |
| 704 Width=1 | |
| 705 Mass Label=1 | |
| 706 Pep Label=0 | |
| 707 [Compare Display] | |
| 708 Neutral Loss=0 | |
| 709 Scale=0 | |
| 710 Min mz=0 | |
| 711 Max mz=1000 | |
| 712 Default Search Anchor=1 | |
| 713 Search Anchor=0 | |
| 714 Default Hit Anchor=1 | |
| 715 Hit Anchor=0 | |
| 716 Max Loss=70 | |
| 717 mz=10 | |
| 718 [SpecList] | |
| 719 Placement_flags=0 | |
| 720 Placement_show=1 | |
| 721 Placement_minx=-1 | |
| 722 Placement_miny=-1 | |
| 723 Placement_maxx=-8 | |
| 724 Placement_maxy=-30 | |
| 725 Placement_left=100 | |
| 726 Placement_top=100 | |
| 727 Placement_right=1319 | |
| 728 Placement_bottom=499 | |
| 729 Splitter=0.333054 | |
| 730 Layout=1 | |
| 731 Plot Splitter=0.5 | |
| 732 Plot Splitter Orientation=0 | |
| 733 List Tab=0 | |
| 734 Spectrum Tab=0 | |
| 735 Column=10 39 39 0 0 0 48 0 0 0 0 | |
| 736 [SpecList Hit] | |
| 737 Font Name=MS Shell Dlg | |
| 738 Font Pts=-8 | |
| 739 Font Width=0 | |
| 740 Font Esc=0 | |
| 741 Font Orientation=0 | |
| 742 Font Weight=400 | |
| 743 Font IUSC=0 | |
| 744 Font PCQP=654311424 | |
| 745 Color=0 255 16711680 16777215 16777215 0 | |
| 746 Order Number=1 | |
| 747 Structure Only=0 | |
| 748 Library=0 | |
| 749 Structure Size=50 | |
| 750 Match=0 | |
| 751 Probability=0 | |
| 752 Reverse Match=0 | |
| 753 Clear History=0 | |
| 754 [SpecList Plot] | |
| 755 Font Name=MS Shell Dlg | |
| 756 Font Pts=-8 | |
| 757 Font Width=0 | |
| 758 Font Esc=0 | |
| 759 Font Orientation=0 | |
| 760 Font Weight=400 | |
| 761 Font IUSC=0 | |
| 762 Font PCQP=654311424 | |
| 763 Color=0 255 16711680 0 255 16777215 | |
| 764 Limits ON=0 | |
| 765 Wrap=0 | |
| 766 MW=0 | |
| 767 CAS=0 | |
| 768 Formula=0 | |
| 769 Threshold=0 | |
| 770 Structure=1 | |
| 771 Width=1 | |
| 772 Mass Label=1 | |
| 773 Pep Label=0 | |
| 774 [SpecList Text] | |
| 775 Font Name=MS Shell Dlg | |
| 776 Font Pts=-8 | |
| 777 Font Width=0 | |
| 778 Font Esc=0 | |
| 779 Font Orientation=0 | |
| 780 Font Weight=400 | |
| 781 Font IUSC=0 | |
| 782 Font PCQP=654311424 | |
| 783 Color=16711680 0 255 8421376 16777215 | |
| 784 Ten Peaks=1 | |
| 785 Compound=1 | |
| 786 Intensity=0 | |
| 787 Synonyms=1 | |
| 788 Rows=0 | |
| 789 Noise=0 | |
| 790 Wrap Synonyms=0 | |
| 791 RI=1 | |
| 792 RI All=1 | |
| 793 RI Num=2 | |
| 794 [BAR-Bar0] | |
| 795 BarID=59419 | |
| 796 Bars=5 | |
| 797 Bar#0=0 | |
| 798 Bar#1=59647 | |
| 799 Bar#2=0 | |
| 800 Bar#3=59392 | |
| 801 Bar#4=0 | |
| 802 [BAR-Bar1] | |
| 803 BarID=59393 | |
| 804 MRUWidth=0 | |
| 805 [BAR-Bar2] | |
| 806 BarID=59647 | |
| 807 MRUWidth=288 | |
| 808 Docking=1 | |
| 809 MRUDockID=0 | |
| 810 MRUDockLeftPos=-1 | |
| 811 MRUDockTopPos=-1 | |
| 812 MRUDockRightPos=1599 | |
| 813 MRUDockBottomPos=28 | |
| 814 MRUFloatStyle=8196 | |
| 815 MRUFloatXPos=-2147483648 | |
| 816 MRUFloatYPos=0 | |
| 817 [BAR-Bar3] | |
| 818 BarID=59392 | |
| 819 YPos=28 | |
| 820 MRUWidth=276 | |
| 821 Docking=1 | |
| 822 MRUDockID=0 | |
| 823 MRUDockLeftPos=-1 | |
| 824 MRUDockTopPos=28 | |
| 825 MRUDockRightPos=294 | |
| 826 MRUDockBottomPos=61 | |
| 827 MRUFloatStyle=8196 | |
| 828 MRUFloatXPos=-2147483648 | |
| 829 MRUFloatYPos=0</configfile> | |
| 830 | |
| 831 </configfiles> | |
| 832 | |
| 833 <outputs> | |
| 834 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/> | |
| 3 | 835 <data name="outputFileFinal" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/> |
| 0 | 836 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/> |
| 837 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/> | |
| 838 </outputs> | |
|
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adding code to ignore wine stderr ouptut
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839 <stdio> |
|
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840 <exit_code range="1:" level="fatal" description="Error occurred" /> |
|
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841 </stdio> |
| 0 | 842 <tests> |
| 843 <test> | |
| 844 </test> | |
| 845 </tests> | |
| 846 <help> | |
| 847 | |
| 848 .. class:: infomark | |
| 849 | |
| 850 Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results | |
| 851 file with the library matches found for each input spectrum found in the given spectra file. | |
| 852 | |
| 853 .. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png | |
| 854 | |
| 855 | |
| 856 .. class:: infomark | |
| 857 | |
| 858 This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server. | |
| 859 Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information. | |
| 860 | |
| 861 *References* | |
| 862 | |
| 863 NIST Mass Spectral Search Program (Version 2.2) | |
| 864 | |
| 865 http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf | |
| 866 | |
| 867 | |
| 868 For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library | |
| 869 Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865. | |
| 870 | |
| 871 </help> | |
| 872 </tool> |