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Sign upAdd ElementInclusion Filter command line flag #18
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schymane
commented
Nov 29, 2018
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When I built this into ReSOLUTION I used different options for the elements, can you check if these options work for you (this should point you to the code snippet where it starts)?
https://github.com/schymane/ReSOLUTION/blob/master/R/MetFragConfigR.R#L400
(I hope you can piece it together through the R code ... )
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From: korseby <notifications@github.com>
Sent: 27 November 2018 14:16:25
To: c-ruttkies/MetFragRelaunched
Cc: Subscribed
Subject: [c-ruttkies/MetFragRelaunched] Add ElementInclusion Filter command line flag (#18)
Hi @c-ruttkies<https://github.com/c-ruttkies> , @sneumann<https://github.com/sneumann>
Is there a command line option to metfrag where I can set the ElementInclusionFilter as I can when using the online version (with MetFragWeb) ?
It does not work using a parameter_list-file and also not on the command line, e.g.:
java -Xmx2048m -Xms1024m -jar /usr/local/bin/metfrag.jar ElementInclusionOptionalFilter=C,H,N,O,P,S ElementExclusion=Cl,Br,F MaximumTreeDepth=2 DatabaseSearchRelativeMassDeviation=10 FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=10 MetFragDatabaseType=PubChem MetFragScoreTypes=FragmenterScore NeutralPrecursorMass=250.26855870556 IsPositiveIonMode=True PrecursorIonType=[M+Na]+ MetFragPeakListReader=de.ipbhalle.metfraglib.peaklistreader.FilteredStringTandemMassPeakListReader MetFragCandidateWriter=CSV PeakListString=119.083926794529_362;121.09904610227_967;122.107360953572_160;123.116845549776_756;133.102751722225_203;134.103396537856_102;135.11645610381_1560;137.131245842048_536;147.114782417154_700;149.132467303767_2383;150.138687808224_180;151.147222745419_335;161.130653601526_1336;162.135550225099_159;163.148551984916_4566;164.152193321854_622;165.162139874983_284;175.146640354038_1711;176.151074479567_169;177.162267717908_5490;178.165005190687_685;179.176343004649_221;189.162089614493_3059;190.164569378975_425;191.177031982117_4097;192.181908186112_582;203.177318060807_4672;204.180072382598_653;217.192706780987_4864;218.197383079608_615;231.209184678108_671;232.213936383458_139;245.223786635388_105;273.256112033523_17362;274.259675383408_3020 SampleName=100_911.556_273.2563_219353.328727272_pos_27_winter_Marpol_27_2-E,3_01_17272.mzML.txt
The command line interface exits with ERROR de.ipbhalle.metfrag.commandline.CommandLineTool - Parameter 'ElementInclusionOptionalFilter' not known.
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korseby commentedNov 27, 2018
Hi @c-ruttkies , @sneumann
Is there a command line option to metfrag where I can set the ElementInclusionFilter as I can when using the online version (with MetFragWeb) ?
It does not work using a parameter_list-file and also not on the command line, e.g.:
java -Xmx2048m -Xms1024m -jar /usr/local/bin/metfrag.jar ElementInclusionOptionalFilter=C,H,N,O,P,S ElementExclusion=Cl,Br,F MaximumTreeDepth=2 DatabaseSearchRelativeMassDeviation=10 FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=10 MetFragDatabaseType=PubChem MetFragScoreTypes=FragmenterScore NeutralPrecursorMass=250.26855870556 IsPositiveIonMode=True PrecursorIonType=[M+Na]+ MetFragPeakListReader=de.ipbhalle.metfraglib.peaklistreader.FilteredStringTandemMassPeakListReader MetFragCandidateWriter=CSV PeakListString=119.083926794529_362;121.09904610227_967;122.107360953572_160;123.116845549776_756;133.102751722225_203;134.103396537856_102;135.11645610381_1560;137.131245842048_536;147.114782417154_700;149.132467303767_2383;150.138687808224_180;151.147222745419_335;161.130653601526_1336;162.135550225099_159;163.148551984916_4566;164.152193321854_622;165.162139874983_284;175.146640354038_1711;176.151074479567_169;177.162267717908_5490;178.165005190687_685;179.176343004649_221;189.162089614493_3059;190.164569378975_425;191.177031982117_4097;192.181908186112_582;203.177318060807_4672;204.180072382598_653;217.192706780987_4864;218.197383079608_615;231.209184678108_671;232.213936383458_139;245.223786635388_105;273.256112033523_17362;274.259675383408_3020 SampleName=100_911.556_273.2563_219353.328727272_pos_27_winter_Marpol_27_2-E,3_01_17272.mzML.txtThe command line interface exits with
ERROR de.ipbhalle.metfrag.commandline.CommandLineTool - Parameter 'ElementInclusionOptionalFilter' not known.