--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nist_wrapper.xml	Thu Jan 22 16:14:57 2015 +0100
@@ -0,0 +1,859 @@
+<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>
+	<command interpreter="export DISPLAY=:0; python">
+		nist_wrapper.py
+		"~/.wine/drive_c/NIST"
+		$nistIniFile
+		$spectraFile
+		$outputFile
+	</command>
+<inputs>
+	<param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>
+
+	<param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum" 
+	           help="Top X matches for each spectrum will be written to output file." />
+	
+</inputs>
+<configfiles>
+
+<configfile name="nistIniFile">[MAIN]
+Version=2.0
+Library Directory=C:\NISTDEMO\MSSEARCH\
+Program=NIST MS
+Active Frame=0
+Placement_flags=2
+Placement_show=3
+Placement_minx=-32000
+Placement_miny=-32000
+Placement_maxx=-1
+Placement_maxy=-1
+Placement_left=0
+Placement_top=84
+Placement_right=1440
+Placement_bottom=827
+Wrong Libraries=
+Active Show=3
+Display Warning=1
+Display Info=0
+[Search Options]
+Automatic=1
+Type=1
+As MW=1
+MW=1
+Reverse=0
+Penalize=0
+Search with MW=1
+Preasearch=0
+Apply Limits=0
+Min Mass Type=0
+Min Mass=1
+Max Mass ON=0
+Max Mass=2000
+Min Abund ON=0
+Min Abund=1
+Printing=0
+Return Focus=0
+Hits to Print=${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 ${on_string} - NIST library matches (TSV)"/>
+	<data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
+</outputs>
+<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>
\ No newline at end of file