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comparison nist_wrapper.xml @ 0:cce6989ed423

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new NIST wrapper demo tools
author pieter.lukasse@wur.nl
date Thu, 22 Jan 2015 16:14:57 +0100
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children f6da901ffff8
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-1:000000000000 0:cce6989ed423
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>
8 <command interpreter="export DISPLAY=:0; python">
9 nist_wrapper.py
10 "~/.wine/drive_c/NIST"
11 $nistIniFile
12 $spectraFile
13 $outputFile
14 </command>
15 <inputs>
16 <param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>
17
18 <param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum"
19 help="Top X matches for each spectrum will be written to output file." />
20
21 </inputs>
22 <configfiles>
23
24 <configfile name="nistIniFile">[MAIN]
25 Version=2.0
26 Library Directory=C:\NISTDEMO\MSSEARCH\
27 Program=NIST MS
28 Active Frame=0
29 Placement_flags=2
30 Placement_show=3
31 Placement_minx=-32000
32 Placement_miny=-32000
33 Placement_maxx=-1
34 Placement_maxy=-1
35 Placement_left=0
36 Placement_top=84
37 Placement_right=1440
38 Placement_bottom=827
39 Wrong Libraries=
40 Active Show=3
41 Display Warning=1
42 Display Info=0
43 [Search Options]
44 Automatic=1
45 Type=1
46 As MW=1
47 MW=1
48 Reverse=0
49 Penalize=0
50 Search with MW=1
51 Preasearch=0
52 Apply Limits=0
53 Min Mass Type=0
54 Min Mass=1
55 Max Mass ON=0
56 Max Mass=2000
57 Min Abund ON=0
58 Min Abund=1
59 Printing=0
60 Return Focus=0
61 Hits to Print=${hitsToReport}
62 Print Spectra=1
63 Print Structure=1
64 Apply MaxLength=0
65 MaxLength=2000
66 Sort Mode=0
67 Match Clusters=1
68 Match Rings=1
69 Weighting=0
70 Use Specified Parent=0
71 Ignore Precursor=0
72 Parent Mass=0
73 Precursor Tolerance=1.6
74 Ions Tolerance=0.8
75 [Libraries]
76 Library_0=mainlib
77 Library_1=
78 Library_2=
79 Library_3=
80 Library_4=
81 Library_5=
82 Library_6=
83 Library_7=
84 Library_8=
85 Library_9=
86 Library_10=
87 Library_11=
88 Library_12=
89 Library_13=
90 Library_14=
91 Library_15=
92 Order_0=1 1
93 Order_1=1 1
94 Order_2=1 1
95 Order_3=1 1
96 Order_4=1 1
97 Order_5=1 1
98 Order_6=1 1
99 Order_7=1 1
100 Order_8=1 1
101 Order_9=1 1
102 [ICHI]
103 On=1
104 Isotope=1
105 Stereo=0
106 Derivative=1
107 [Import]
108 Dir=C:\NISTDEMO\MSSEARCH\
109 Synonyms=1
110 Filter=1
111 Coeff=1 0
112 [Structure Import]
113 Dir=C:\NISTDEMO\MSSEARCH\
114 Filter=1
115 [Export]
116 Dir=C:\NISTDEMO\MSSEARCH\
117 Synonyms=1
118 Filter=1
119 Coeff=1 0
120 [Search Options]
121 Automatic=1
122 [Library Search]
123 SpecList Tab=1
124 Placement_flags=2
125 Placement_show=3
126 ;Layout=1
127 ;Hit Splitter Orientation=1
128 ;List Tab=0
129 ;Compare Tab=0
130 ;Hit Tab=0
131 ;Unknown Tab=0
132 Placement_minx=-1
133 Placement_miny=-1
134 ;Placement_maxx=-4
135 Placement_maxx=-8
136 ;Placement_maxy=-23
137 Placement_maxy=-30
138 Placement_left=0
139 Placement_top=1
140 Placement_right=678
141 Placement_bottom=397
142 Splitter=0.314139
143 List Splitter=0 0
144 Unknown Splitter=0.493119
145 Unknown Splitter Orientation=1
146 ;Compare Splitter=0.3333 0.3333
147 Compare Splitter=0 0
148 Hit Splitter=0.493874
149 SpecList Splitter=0.493119
150 SpecList Splitter Orientation=1
151 Hits Column=10 41 39 58 68 56 256 0 0 0 0
152 ;SpecList Column=3 41 41 56
153 ;SpecList Column=3 41 41 156
154 SpecList Column=10 41 38 128 0 0 48 0 0 0 0
155 Layout=1
156 Hit Splitter Orientation=1
157 List Tab=0
158 Compare Tab=0
159 Hit Tab=0
160 Unknown Tab=0
161 Replicates=0
162 Exact Match=0
163 [BAR-Summary]
164 Bars=4
165 ScreenCX=1600
166 ScreenCY=900
167 [REPORT]
168 Ten Largest Peaks=1
169 Compound Info=1
170 Mass Intensity List=0
171 Synonyms=1
172 Plot=1
173 Structure=1
174 First Hits=1
175 First Hits Number=3
176 Unknown=0
177 [Substructure Export]
178 Filter=1
179 Dir=
180 [Substructure Import]
181 Filter=1
182 Dir=
183 [Search AnyPeaks Options]
184 Other=0
185 Peaks=0
186 Hitlist size=100
187 Peak0=
188 Peak1=
189 Peak2=
190 Peak3=
191 Peak4=
192 Peak5=
193 Peak6=
194 Peak7=
195 Peak8=
196 Peak9=
197 Peak10=
198 [Other Searches Options]
199 CAS=
200 MW=1
201 ID=
202 EPA=
203 Formula=
204 Seq Hitlist size=100
205 [Constraints]
206 Library ON=0
207 Formula ON=0
208 MW ON=0
209 AnyPeaks ON=0
210 Sequentiial ON=0
211 Active MW=0
212 MINMW=1
213 MAXMW=2000
214 Active Name=0
215 Name Fragment=
216 Elements Value=0
217 Elements Present=0
218 Mode Elements=0
219 Num Elements=0
220 Elements0=
221 Elements1=
222 Elements2=
223 Elements3=
224 Elements4=
225 Elements5=
226 Elements6=
227 Elements7=
228 Elements8=
229 Elements9=
230 Num Compare Elements=0
231 Compare Elements0=
232 Compare Elements1=
233 Compare Elements2=
234 Compare Elements3=
235 Compare Elements4=
236 Compare Elements5=
237 Compare Elements6=
238 Compare Elements7=
239 Compare Elements8=
240 Compare Elements9=
241 Active Peaks=0
242 Mode Peaks=1
243 Num AnyPeaks=0
244 Active OtherDB=0
245 OtherDB=0
246 Active Tags=0
247 Tags=
248 Active Peptide Sequence=0
249 Peptide Sequence=
250 Active Proton=0
251 Proton Mode=0
252 Proton Low=
253 Proton Hi=
254 Proton Exact=
255 Active Charge=0
256 Charge Mode=0
257 Charge Low=
258 Charge Hi=
259 Charge Exact=
260 Active Residue=0
261 Residue Mode=0
262 Residue Low=
263 Residue Hi=
264 Residue Exact=
265 [Peptide Search Options]
266 Cysteine Modification=0
267 Comment Fields=
268 Show Fields On Plot=1
269 TF qry=0
270 E Omssa=0
271 TF lib=0
272 RevImp=0
273 Weight Omssa=0
274 Weight Num Rep=0
275 Weight Qtof=0
276 Treshold=0
277 [Library Hit]
278 Font Name=MS Shell Dlg
279 Font Pts=-8
280 Font Width=0
281 Font Esc=0
282 Font Orientation=0
283 Font Weight=400
284 Font IUSC=0
285 Font PCQP=654311424
286 Color=0 255 16711680 16777215 16777215 0
287 Order Number=1
288 Structure Only=0
289 Library=0
290 Structure Size=50
291 Match=1
292 Probability=1
293 Reverse Match=1
294 Clear History=0
295 [Library Spec List]
296 Font Name=MS Shell Dlg
297 Font Pts=-8
298 Font Width=0
299 Font Esc=0
300 Font Orientation=0
301 Font Weight=400
302 Font IUSC=0
303 Font PCQP=654311424
304 Color=0 255 16711680 16777215 16777215 0
305 Order Number=1
306 Structure Only=0
307 Library=0
308 Structure Size=50
309 Match=0
310 Probability=0
311 Reverse Match=0
312 Clear History=0
313 [Library Unknown Plot]
314 Font Name=MS Shell Dlg
315 Font Pts=-8
316 Font Width=0
317 Font Esc=0
318 Font Orientation=0
319 Font Weight=400
320 Font IUSC=0
321 Font PCQP=654311424
322 Color=0 255 16711680 0 255 16777215
323 Limits ON=0
324 Wrap=0
325 MW=0
326 CAS=0
327 Formula=0
328 Threshold=0
329 Structure=1
330 Width=1
331 Mass Label=1
332 Pep Label=0
333 [Library Hit Plot]
334 Font Name=MS Shell Dlg
335 Font Pts=-8
336 Font Width=0
337 Font Esc=0
338 Font Orientation=0
339 Font Weight=400
340 Font IUSC=0
341 Font PCQP=654311424
342 Color=0 255 16711680 0 255 16777215
343 Limits ON=0
344 Wrap=0
345 MW=1
346 CAS=0
347 Formula=1
348 Threshold=0
349 Structure=1
350 Width=1
351 Mass Label=1
352 Pep Label=0
353 [Library SpecList Plot]
354 Font Name=MS Shell Dlg
355 Font Pts=-8
356 Font Width=0
357 Font Esc=0
358 Font Orientation=0
359 Font Weight=400
360 Font IUSC=0
361 Font PCQP=654311424
362 Color=0 255 16711680 0 255 16777215
363 Limits ON=0
364 Wrap=0
365 MW=0
366 CAS=0
367 Formula=0
368 Threshold=0
369 Structure=1
370 Width=1
371 Mass Label=1
372 Pep Label=0
373 [Library Unknown Text]
374 Font Name=MS Shell Dlg
375 Font Pts=-8
376 Font Width=0
377 Font Esc=0
378 Font Orientation=0
379 Font Weight=400
380 Font IUSC=0
381 Font PCQP=654311424
382 Color=16711680 0 255 8421376 16777215
383 Ten Peaks=1
384 Compound=1
385 Intensity=0
386 Synonyms=1
387 Rows=0
388 Noise=0
389 Wrap Synonyms=0
390 RI=1
391 RI All=1
392 RI Num=2
393 [Library Hit Text]
394 Font Name=MS Shell Dlg
395 Font Pts=-8
396 Font Width=0
397 Font Esc=0
398 Font Orientation=0
399 Font Weight=400
400 Font IUSC=0
401 Font PCQP=654311424
402 Color=16711680 0 255 8421376 16777215
403 Ten Peaks=1
404 Compound=1
405 Intensity=1
406 Synonyms=1
407 Rows=0
408 Noise=0
409 Wrap Synonyms=0
410 RI=1
411 RI All=1
412 RI Num=2
413 [Library SpecList Text]
414 Font Name=MS Shell Dlg
415 Font Pts=-8
416 Font Width=0
417 Font Esc=0
418 Font Orientation=0
419 Font Weight=400
420 Font IUSC=0
421 Font PCQP=654311424
422 Color=16711680 0 255 8421376 16777215
423 Ten Peaks=1
424 Compound=1
425 Intensity=0
426 Synonyms=1
427 Rows=0
428 Noise=0
429 Wrap Synonyms=0
430 RI=1
431 RI All=1
432 RI Num=2
433 [Library Compare]
434 Font Name=MS Shell Dlg
435 Font Pts=-8
436 Font Width=0
437 Font Esc=0
438 Font Orientation=0
439 Font Weight=400
440 Font IUSC=0
441 Font PCQP=654311424
442 Color=0 255 16711680 32768 16777215
443 Limit ON=0
444 Threshold=0
445 Show=1
446 Show Structure=0
447 Independent Zoom=0
448 Width=1
449 [Library Histogram]
450 Font Name=MS Shell Dlg
451 Font Pts=-8
452 Font Width=0
453 Font Esc=0
454 Font Orientation=0
455 Font Weight=400
456 Font IUSC=0
457 Font PCQP=654311424
458 Color=0 16711680 255 16777215
459 Discret=25
460 Axis=1
461 Automatic=1
462 Min=0
463 Max=1000
464 [Library Display]
465 Neutral Loss=0
466 Scale=0
467 Min mz=0
468 Max mz=1000
469 Default Search Anchor=1
470 Search Anchor=0
471 Default Hit Anchor=1
472 Hit Anchor=0
473 Max Loss=70
474 mz=10
475 [Incremental Search]
476 Placement_flags=0
477 Placement_show=1
478 Placement_minx=-1
479 Placement_miny=-1
480 Placement_maxx=-8
481 Placement_maxy=-30
482 Placement_left=50
483 Placement_top=50
484 Placement_right=1269
485 Placement_bottom=449
486 Key=10METHOXYDESERPID
487 Splitter=0.333054
488 Layout=1
489 Plot Splitter=0.5
490 Plot Splitter Orientation=0
491 List Tab=0
492 Spectrum Tab=0
493 Alpha=0
494 [Incremental View]
495 Font Name=MS Shell Dlg
496 Font Pts=-8
497 Font Width=0
498 Font Esc=0
499 Font Orientation=0
500 Font Weight=400
501 Font IUSC=0
502 Font PCQP=654311424
503 Color=0 255 16711680 16777215 16777215 0
504 Auto Display=1
505 Structure Only=50
506 [Incremental Plot]
507 Font Name=MS Shell Dlg
508 Font Pts=-8
509 Font Width=0
510 Font Esc=0
511 Font Orientation=0
512 Font Weight=400
513 Font IUSC=0
514 Font PCQP=654311424
515 Color=0 255 16711680 0 255 16777215
516 Limits ON=0
517 Wrap=0
518 MW=0
519 CAS=0
520 Formula=0
521 Threshold=0
522 Structure=1
523 Width=1
524 Mass Label=1
525 Pep Label=0
526 [Incremental Text]
527 Font Name=MS Shell Dlg
528 Font Pts=-8
529 Font Width=0
530 Font Esc=0
531 Font Orientation=0
532 Font Weight=400
533 Font IUSC=0
534 Font PCQP=654311424
535 Color=16711680 0 255 8421376 16777215
536 Ten Peaks=1
537 Compound=1
538 Intensity=0
539 Synonyms=1
540 Rows=0
541 Noise=0
542 Wrap Synonyms=0
543 RI=1
544 RI All=1
545 RI Num=2
546 [Other Search]
547 Placement_flags=0
548 Placement_show=1
549 Placement_minx=-1
550 Placement_miny=-1
551 Placement_maxx=-8
552 Placement_maxy=-30
553 Placement_left=25
554 Placement_top=25
555 Placement_right=1244
556 Placement_bottom=424
557 Splitter=0.332215
558 Layout=1
559 Plot Splitter=0.5
560 Plot Splitter Orientation=0
561 List Tab=0
562 Spectrum Tab=0
563 Replicates=0
564 Search Mode=2
565 Column=10 39 37 0 0 0 48 0 0 0 0
566 [Other Hit]
567 Font Name=MS Shell Dlg
568 Font Pts=-8
569 Font Width=0
570 Font Esc=0
571 Font Orientation=0
572 Font Weight=400
573 Font IUSC=0
574 Font PCQP=654311424
575 Color=0 255 16711680 16777215 16777215 0
576 Order Number=1
577 Structure Only=0
578 Library=0
579 Structure Size=50
580 Match=0
581 Probability=0
582 Reverse Match=0
583 Clear History=0
584 [Other Plot]
585 Font Name=MS Shell Dlg
586 Font Pts=-8
587 Font Width=0
588 Font Esc=0
589 Font Orientation=0
590 Font Weight=400
591 Font IUSC=0
592 Font PCQP=654311424
593 Color=0 255 16711680 0 255 16777215
594 Limits ON=0
595 Wrap=0
596 MW=0
597 CAS=0
598 Formula=0
599 Threshold=0
600 Structure=1
601 Width=1
602 Mass Label=1
603 Pep Label=0
604 [Other Text]
605 Font Name=MS Shell Dlg
606 Font Pts=-8
607 Font Width=0
608 Font Esc=0
609 Font Orientation=0
610 Font Weight=400
611 Font IUSC=0
612 Font PCQP=654311424
613 Color=16711680 0 255 8421376 16777215
614 Ten Peaks=1
615 Compound=1
616 Intensity=0
617 Synonyms=1
618 Rows=0
619 Noise=0
620 Wrap Synonyms=0
621 RI=1
622 RI All=1
623 RI Num=2
624 [Compare]
625 Placement_flags=0
626 Placement_show=1
627 Placement_minx=-1
628 Placement_miny=-1
629 Placement_maxx=-8
630 Placement_maxy=-30
631 Placement_left=75
632 Placement_top=75
633 Placement_right=1294
634 Placement_bottom=474
635 Splitter=0.244898 0.244898
636 Tab=0
637 [Compare Plot]
638 Font Name=MS Shell Dlg
639 Font Pts=-8
640 Font Width=0
641 Font Esc=0
642 Font Orientation=0
643 Font Weight=400
644 Font IUSC=0
645 Font PCQP=654311424
646 Color=0 255 16711680 0 255 16777215
647 Limits ON=0
648 Wrap=0
649 MW=0
650 CAS=0
651 Formula=0
652 Threshold=0
653 Structure=1
654 Width=1
655 Mass Label=1
656 Pep Label=0
657 [Compare Result]
658 Font Name=MS Shell Dlg
659 Font Pts=-8
660 Font Width=0
661 Font Esc=0
662 Font Orientation=0
663 Font Weight=400
664 Font IUSC=0
665 Font PCQP=654311424
666 Color=0 255 16711680 32768 16777215
667 Limit ON=0
668 Threshold=0
669 Show=1
670 Show Structure=0
671 Independent Zoom=0
672 Width=1
673 [Compare List]
674 Font Name=MS Shell Dlg
675 Font Pts=-8
676 Font Width=0
677 Font Esc=0
678 Font Orientation=0
679 Font Weight=400
680 Font IUSC=0
681 Font PCQP=654311424
682 Color=32768 0 255 16711680 16777215 0 255
683 Names=1
684 No Structure=0
685 Limits ON=0
686 Threshold=0
687 Spectra on Page=3
688 Overwrite=1
689 Insert=1
690 Hits=3
691 Wrap=0
692 MW=0
693 CAS=0
694 Formula=0
695 Width=1
696 Mass Label=1
697 Pep Label=0
698 [Compare Display]
699 Neutral Loss=0
700 Scale=0
701 Min mz=0
702 Max mz=1000
703 Default Search Anchor=1
704 Search Anchor=0
705 Default Hit Anchor=1
706 Hit Anchor=0
707 Max Loss=70
708 mz=10
709 [SpecList]
710 Placement_flags=0
711 Placement_show=1
712 Placement_minx=-1
713 Placement_miny=-1
714 Placement_maxx=-8
715 Placement_maxy=-30
716 Placement_left=100
717 Placement_top=100
718 Placement_right=1319
719 Placement_bottom=499
720 Splitter=0.333054
721 Layout=1
722 Plot Splitter=0.5
723 Plot Splitter Orientation=0
724 List Tab=0
725 Spectrum Tab=0
726 Column=10 39 39 0 0 0 48 0 0 0 0
727 [SpecList Hit]
728 Font Name=MS Shell Dlg
729 Font Pts=-8
730 Font Width=0
731 Font Esc=0
732 Font Orientation=0
733 Font Weight=400
734 Font IUSC=0
735 Font PCQP=654311424
736 Color=0 255 16711680 16777215 16777215 0
737 Order Number=1
738 Structure Only=0
739 Library=0
740 Structure Size=50
741 Match=0
742 Probability=0
743 Reverse Match=0
744 Clear History=0
745 [SpecList Plot]
746 Font Name=MS Shell Dlg
747 Font Pts=-8
748 Font Width=0
749 Font Esc=0
750 Font Orientation=0
751 Font Weight=400
752 Font IUSC=0
753 Font PCQP=654311424
754 Color=0 255 16711680 0 255 16777215
755 Limits ON=0
756 Wrap=0
757 MW=0
758 CAS=0
759 Formula=0
760 Threshold=0
761 Structure=1
762 Width=1
763 Mass Label=1
764 Pep Label=0
765 [SpecList Text]
766 Font Name=MS Shell Dlg
767 Font Pts=-8
768 Font Width=0
769 Font Esc=0
770 Font Orientation=0
771 Font Weight=400
772 Font IUSC=0
773 Font PCQP=654311424
774 Color=16711680 0 255 8421376 16777215
775 Ten Peaks=1
776 Compound=1
777 Intensity=0
778 Synonyms=1
779 Rows=0
780 Noise=0
781 Wrap Synonyms=0
782 RI=1
783 RI All=1
784 RI Num=2
785 [BAR-Bar0]
786 BarID=59419
787 Bars=5
788 Bar#0=0
789 Bar#1=59647
790 Bar#2=0
791 Bar#3=59392
792 Bar#4=0
793 [BAR-Bar1]
794 BarID=59393
795 MRUWidth=0
796 [BAR-Bar2]
797 BarID=59647
798 MRUWidth=288
799 Docking=1
800 MRUDockID=0
801 MRUDockLeftPos=-1
802 MRUDockTopPos=-1
803 MRUDockRightPos=1599
804 MRUDockBottomPos=28
805 MRUFloatStyle=8196
806 MRUFloatXPos=-2147483648
807 MRUFloatYPos=0
808 [BAR-Bar3]
809 BarID=59392
810 YPos=28
811 MRUWidth=276
812 Docking=1
813 MRUDockID=0
814 MRUDockLeftPos=-1
815 MRUDockTopPos=28
816 MRUDockRightPos=294
817 MRUDockBottomPos=61
818 MRUFloatStyle=8196
819 MRUFloatXPos=-2147483648
820 MRUFloatYPos=0</configfile>
821
822 </configfiles>
823
824 <outputs>
825 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
826 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
827 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
828 </outputs>
829 <tests>
830 <test>
831 </test>
832 </tests>
833 <help>
834
835 .. class:: infomark
836
837 Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results
838 file with the library matches found for each input spectrum found in the given spectra file.
839
840 .. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png
841
842
843 .. class:: infomark
844
845 This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server.
846 Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information.
847
848 *References*
849
850 NIST Mass Spectral Search Program (Version 2.2)
851
852 http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf
853
854
855 For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library
856 Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865.
857
858 </help>
859 </tool>