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killing nist at exception
author pieter.lukasse@wur.nl
date Fri, 23 Jan 2015 17:57:00 +0100
parents 92cf554fca03
children
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<tool id="nist_wrapper" name="NIST MSSEARCH"  version="0.0.1">
	<!-- 
	   This part is a WORKAROUND for the wine X11 dependency, allowing it to run headless :
	    -> install Xvfb and enable it on a port, say 995:
	    -> make sure this gets executed: export DISPLAY=:995;
	    -->
	<description> Runs NIST's msseach program to match spectra against metabolite libraries</description>
	
    <requirements>
      <requirement name="package" version="0.2">nist_wrapper_venv</requirement>
    </requirements>	
	
	<command interpreter="export DISPLAY=:995; python">
		nist_wrapper.py
		"/home/galaxy/.wine/drive_c/NIST"
		$nistIniFile
		$spectraFile
		$outputFile
		$outputFileFinal
		$outputLog
		$htmlReportFile
		$htmlReportFile.files_path
	</command>
<inputs>
	<param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>

	<param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum" 
	           help="Top X matches for each spectrum will be written to output file." />
	
</inputs>
<configfiles>

<configfile name="nistIniFile">[MAIN]
Version=2.0
Library Directory=C:\NISTDEMO\MSSEARCH\
Program=NIST MS
Active Frame=0
Placement_flags=2
Placement_show=3
Placement_minx=-32000
Placement_miny=-32000
Placement_maxx=-1
Placement_maxy=-1
Placement_left=0
Placement_top=84
Placement_right=1440
Placement_bottom=827
Wrong Libraries=
Active Show=3
Display Warning=1
Display Info=0
[Search Options]
Automatic=1
Type=1
As MW=1
MW=1
Reverse=0
Penalize=0
Search with MW=1
Preasearch=0
Apply Limits=0
Min Mass Type=0
Min Mass=1
Max Mass ON=0
Max Mass=2000
Min Abund ON=0
Min Abund=1
Printing=0
Return Focus=0
Hits to Print=${hitsToReport}
Print Spectra=1
Print Structure=1
Apply MaxLength=0
MaxLength=2000
Sort Mode=0
Match Clusters=1
Match Rings=1
Weighting=0
Use Specified Parent=0
Ignore Precursor=0
Parent Mass=0
Precursor Tolerance=1.6
Ions Tolerance=0.8
[Libraries]
Library_0=mainlib
Library_1=
Library_2=
Library_3=
Library_4=
Library_5=
Library_6=
Library_7=
Library_8=
Library_9=
Library_10=
Library_11=
Library_12=
Library_13=
Library_14=
Library_15=
Order_0=1 1
Order_1=1 1
Order_2=1 1
Order_3=1 1
Order_4=1 1
Order_5=1 1
Order_6=1 1
Order_7=1 1
Order_8=1 1
Order_9=1 1
[ICHI]
On=1
Isotope=1
Stereo=0
Derivative=1
[Import]
Dir=C:\NISTDEMO\MSSEARCH\
Synonyms=1
Filter=1
Coeff=1 0
[Structure Import]
Dir=C:\NISTDEMO\MSSEARCH\
Filter=1
[Export]
Dir=C:\NISTDEMO\MSSEARCH\
Synonyms=1
Filter=1
Coeff=1 0
[Search Options]
Automatic=1
[Library Search]
SpecList Tab=1
Placement_flags=2
Placement_show=3
;Layout=1
;Hit Splitter Orientation=1
;List Tab=0
;Compare Tab=0
;Hit Tab=0
;Unknown Tab=0
Placement_minx=-1
Placement_miny=-1
;Placement_maxx=-4
Placement_maxx=-8
;Placement_maxy=-23
Placement_maxy=-30
Placement_left=0
Placement_top=1
Placement_right=678
Placement_bottom=397
Splitter=0.314139
List Splitter=0 0
Unknown Splitter=0.493119
Unknown Splitter Orientation=1
;Compare Splitter=0.3333 0.3333
Compare Splitter=0 0
Hit Splitter=0.493874
SpecList Splitter=0.493119
SpecList Splitter Orientation=1
Hits Column=10 41 39 58 68 56 256 0 0 0 0
;SpecList Column=3 41 41 56
;SpecList Column=3 41 41 156
SpecList Column=10 41 38 128 0 0 48 0 0 0 0
Layout=1
Hit Splitter Orientation=1
List Tab=0
Compare Tab=0
Hit Tab=0
Unknown Tab=0
Replicates=0
Exact Match=0
[BAR-Summary]
Bars=4
ScreenCX=1600
ScreenCY=900
[REPORT]
Ten Largest Peaks=1
Compound Info=1
Mass Intensity List=0
Synonyms=1
Plot=1
Structure=1
First Hits=1
First Hits Number=3
Unknown=0
[Substructure Export]
Filter=1
Dir=
[Substructure Import]
Filter=1
Dir=
[Search AnyPeaks Options]
Other=0
Peaks=0
Hitlist size=100
Peak0=
Peak1=
Peak2=
Peak3=
Peak4=
Peak5=
Peak6=
Peak7=
Peak8=
Peak9=
Peak10=
[Other Searches Options]
CAS=
MW=1
ID=
EPA=
Formula=
Seq Hitlist size=100
[Constraints]
Library ON=0
Formula ON=0
MW ON=0
AnyPeaks ON=0
Sequentiial ON=0
Active MW=0
MINMW=1
MAXMW=2000
Active Name=0
Name Fragment=
Elements Value=0
Elements Present=0
Mode Elements=0
Num Elements=0
Elements0=
Elements1=
Elements2=
Elements3=
Elements4=
Elements5=
Elements6=
Elements7=
Elements8=
Elements9=
Num Compare Elements=0
Compare Elements0=
Compare Elements1=
Compare Elements2=
Compare Elements3=
Compare Elements4=
Compare Elements5=
Compare Elements6=
Compare Elements7=
Compare Elements8=
Compare Elements9=
Active Peaks=0
Mode Peaks=1
Num AnyPeaks=0
Active OtherDB=0
OtherDB=0
Active Tags=0
Tags=
Active Peptide Sequence=0
Peptide Sequence=
Active Proton=0
Proton Mode=0
Proton Low=
Proton Hi=
Proton Exact=
Active Charge=0
Charge Mode=0
Charge Low=
Charge Hi=
Charge Exact=
Active Residue=0
Residue Mode=0
Residue Low=
Residue Hi=
Residue Exact=
[Peptide Search Options]
Cysteine Modification=0
Comment Fields=
Show Fields On Plot=1
TF qry=0
E Omssa=0
TF lib=0
RevImp=0
Weight Omssa=0
Weight Num Rep=0
Weight Qtof=0
Treshold=0
[Library Hit]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 16777215 16777215 0
Order Number=1
Structure Only=0
Library=0
Structure Size=50
Match=1
Probability=1
Reverse Match=1
Clear History=0
[Library Spec List]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 16777215 16777215 0
Order Number=1
Structure Only=0
Library=0
Structure Size=50
Match=0
Probability=0
Reverse Match=0
Clear History=0
[Library Unknown Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Library Hit Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=1
CAS=0
Formula=1
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Library SpecList Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Library Unknown Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=0
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[Library Hit Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=1
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[Library SpecList Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=0
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[Library Compare]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 32768 16777215
Limit ON=0
Threshold=0
Show=1
Show Structure=0
Independent Zoom=0
Width=1
[Library Histogram]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 16711680 255 16777215
Discret=25
Axis=1
Automatic=1
Min=0
Max=1000
[Library Display]
Neutral Loss=0
Scale=0
Min mz=0
Max mz=1000
Default Search Anchor=1
Search Anchor=0
Default Hit Anchor=1
Hit Anchor=0
Max Loss=70
mz=10
[Incremental Search]
Placement_flags=0
Placement_show=1
Placement_minx=-1
Placement_miny=-1
Placement_maxx=-8
Placement_maxy=-30
Placement_left=50
Placement_top=50
Placement_right=1269
Placement_bottom=449
Key=10METHOXYDESERPID
Splitter=0.333054
Layout=1
Plot Splitter=0.5
Plot Splitter Orientation=0
List Tab=0
Spectrum Tab=0
Alpha=0
[Incremental View]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 16777215 16777215 0
Auto Display=1
Structure Only=50
[Incremental Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Incremental Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=0
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[Other Search]
Placement_flags=0
Placement_show=1
Placement_minx=-1
Placement_miny=-1
Placement_maxx=-8
Placement_maxy=-30
Placement_left=25
Placement_top=25
Placement_right=1244
Placement_bottom=424
Splitter=0.332215
Layout=1
Plot Splitter=0.5
Plot Splitter Orientation=0
List Tab=0
Spectrum Tab=0
Replicates=0
Search Mode=2
Column=10 39 37 0 0 0 48 0 0 0 0
[Other Hit]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 16777215 16777215 0
Order Number=1
Structure Only=0
Library=0
Structure Size=50
Match=0
Probability=0
Reverse Match=0
Clear History=0
[Other Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Other Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=0
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[Compare]
Placement_flags=0
Placement_show=1
Placement_minx=-1
Placement_miny=-1
Placement_maxx=-8
Placement_maxy=-30
Placement_left=75
Placement_top=75
Placement_right=1294
Placement_bottom=474
Splitter=0.244898 0.244898
Tab=0
[Compare Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[Compare Result]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 32768 16777215
Limit ON=0
Threshold=0
Show=1
Show Structure=0
Independent Zoom=0
Width=1
[Compare List]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=32768 0 255 16711680 16777215 0 255
Names=1
No Structure=0
Limits ON=0
Threshold=0
Spectra on Page=3
Overwrite=1
Insert=1
Hits=3
Wrap=0
MW=0
CAS=0
Formula=0
Width=1
Mass Label=1
Pep Label=0
[Compare Display]
Neutral Loss=0
Scale=0
Min mz=0
Max mz=1000
Default Search Anchor=1
Search Anchor=0
Default Hit Anchor=1
Hit Anchor=0
Max Loss=70
mz=10
[SpecList]
Placement_flags=0
Placement_show=1
Placement_minx=-1
Placement_miny=-1
Placement_maxx=-8
Placement_maxy=-30
Placement_left=100
Placement_top=100
Placement_right=1319
Placement_bottom=499
Splitter=0.333054
Layout=1
Plot Splitter=0.5
Plot Splitter Orientation=0
List Tab=0
Spectrum Tab=0
Column=10 39 39 0 0 0 48 0 0 0 0
[SpecList Hit]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 16777215 16777215 0
Order Number=1
Structure Only=0
Library=0
Structure Size=50
Match=0
Probability=0
Reverse Match=0
Clear History=0
[SpecList Plot]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=0 255 16711680 0 255 16777215
Limits ON=0
Wrap=0
MW=0
CAS=0
Formula=0
Threshold=0
Structure=1
Width=1
Mass Label=1
Pep Label=0
[SpecList Text]
Font Name=MS Shell Dlg
Font Pts=-8
Font Width=0
Font Esc=0
Font Orientation=0
Font Weight=400
Font IUSC=0
Font PCQP=654311424
Color=16711680 0 255 8421376 16777215
Ten Peaks=1
Compound=1
Intensity=0
Synonyms=1
Rows=0
Noise=0
Wrap Synonyms=0
RI=1
RI All=1
RI Num=2
[BAR-Bar0]
BarID=59419
Bars=5
Bar#0=0
Bar#1=59647
Bar#2=0
Bar#3=59392
Bar#4=0
[BAR-Bar1]
BarID=59393
MRUWidth=0
[BAR-Bar2]
BarID=59647
MRUWidth=288
Docking=1
MRUDockID=0
MRUDockLeftPos=-1
MRUDockTopPos=-1
MRUDockRightPos=1599
MRUDockBottomPos=28
MRUFloatStyle=8196
MRUFloatXPos=-2147483648
MRUFloatYPos=0
[BAR-Bar3]
BarID=59392
YPos=28
MRUWidth=276
Docking=1
MRUDockID=0
MRUDockLeftPos=-1
MRUDockTopPos=28
MRUDockRightPos=294
MRUDockBottomPos=61
MRUFloatStyle=8196
MRUFloatXPos=-2147483648
MRUFloatYPos=0</configfile>

</configfiles>

<outputs>
	<data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
	<data name="outputFileFinal" format="nist.tsv" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
</outputs>
<stdio>	
	<exit_code range="1:"  level="fatal"   description="Error occurred" />
</stdio>
<tests>
	<test>
	</test>
</tests>
<help>

.. class:: infomark
  
Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results 
file with the library matches found for each input spectrum found in the given spectra file. 

.. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png 


.. class:: infomark

This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server. 
Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information. 

*References*

NIST Mass Spectral Search Program (Version 2.2)

http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf


For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library 
Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865.

  </help>
</tool>