Mercurial > repos > pieterlukasse > nist_wrapper
annotate nist_wrapper.xml @ 17:82368bd06e1d
small improvements
author | pieter.lukasse@wur.nl |
---|---|
date | Fri, 23 Jan 2015 17:13:06 +0100 |
parents | 92cf554fca03 |
children |
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 ${on_string} - NIST library matches (TSV)"/> | |
14 | 835 <data name="outputFileFinal" format="nist.tsv" label="${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> | |
13
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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> |