Mercurial > repos > jjohnson > encyclopedia_fasta_to_prosit_csv
diff macros.xml @ 0:d0202c597434 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 19 Jun 2020 10:21:58 -0400 |
| parents | |
| children | c394bccd6f64 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jun 19 10:21:58 2020 -0400 @@ -0,0 +1,589 @@ +<macros> +<!-- +# generate a Walnut CLIB from GPF-DIA and a FASTA +for i in library/*.mzML; do + java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -walnut -i $i -f uniprot_yeast_25jan2019.fasta; +done +java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -walnut -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; + +# process single-injection DIA with the CLIB +for i in quant/*.mzML; do + java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; +done + +Next for Prosit: +# generate an EncyclopeDIA CLIB from GPF-DIA and a Prosit Library +for i in library/*.mzML; do + java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l prosit_library.dlib -f uniprot_yeast_25jan2019.fasta; +done +java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; + +# process single-injection DIA with the CLIB (exactly the same as with Walnut) +for i in quant/*.mzML; do + java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; +done +--> + <token name="@VERSION@">0.9.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">encyclopedia</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-018-07454-w</citation> + <citation type="doi">10.1038/s41467-020-15346-1</citation> + <yield /> + </citations> + </xml> + <token name="@CMD_IMPORTS@"> +#import re +#def identifier_or_name($input1) + #if hasattr($input1, 'element_identifier') + #return $input1.element_identifier + #else + #return $input1.name + #end if +#end def +#def clean($name1) + ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz')))) + ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz'))) + #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #return $name_clean +#end def +#def ln_name($ds) + #set $ext = '' + #if $ds.is_of_type('mzml') + #set $ext = ".mzML" + #else if $ds.is_of_type('elib') + #set $ext = ".elib" + #else if $ds.is_of_type('dlib') + #set $ext = ".dlib" + #else if $ds.is_of_type('blib') + #set $ext = ".blib" + #else if $ds.is_of_type('fasta') + #set $ext = ".fasta" + #else if $ds.is_of_type('fasta.gz') + #set $ext = ".fasta.gz" + #end if + #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) + #return $name +#end def +#set $i_name = None +#set $f_name = None +#set $l_name = None +#set $t_name = None + </token> + + <xml name="scan_input"> + <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file, .mzml or .dia"/> + </xml> + <token name="@LINK_SCAN_INPUT@"><![CDATA[ + #set $i_name = $ln_name($i) + ln -s '$i' '$i_name' && + ]]></token> + <token name="@SCAN_INPUT@"> + -i '$i_name' + </token> + + <xml name="scan_inputs"> + <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum file, .mzml or .dia"/> + </xml> + <token name="@LINK_SCAN_INPUTS@"><![CDATA[ + #set $inputs_dir = 'inputs' + mkdir -p $inputs_dir && + #for $sf in $i + #set $i_name = $ln_name($sf) + ln -s '$sf' '${inputs_dir}/${i_name}' && + #end for + ]]></token> + <token name="@SCAN_INPUTS@"> + -i '$inputs_dir' + </token> + + <xml name="fasta_input"> + <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/> + </xml> + <token name="@LINK_FASTA_INPUT@"><![CDATA[ + #set $f_name = $ln_name($f) + ln -s '$f' '$f_name' && + ]]></token> + <token name="@FASTA_INPUT@"> + -f '$f_name' + </token> + + <xml name="target_fasta"> + <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/> + <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> + </xml> + <token name="@LINK_TARGET_FASTA@"><![CDATA[ + #if $t + #set $t_name = $ln_name($t) + ln -s '$t' '$t_name' && + #else + #set $t_name = None + #end if + ]]></token> + <token name="@TARGET_FASTA@"> + #if $t_name + -t '$t_name' + -tp $tp + #end if + </token> + + <xml name="lib_input" token_optional="true" token_help=""> + <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> + <help>@HELP@</help> + </param> + </xml> + <token name="@LINK_LIB_INPUT@"><![CDATA[ + #if $l + #set $l_name = $ln_name($l) + cp '$l' $l_name && + #else + #set $l_name = None + #end if + ]]></token> + <token name="@LIB_INPUT@"> + #if $l_name + -l '$l_name' + #end if + </token> + + <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false" + token_cid_selected="false" token_hcd_selected="false"> + <conditional name="acquisition"> + <param name="set_acquisition" type="select" label="Set Acquisition Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> + <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type"> + <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option> + <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option> + </param> + <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme"> + <option value="Trypsin">Trypsin</option> + <option value="Trypsin/p">Trypsin/p</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Arg-C">Arg-C</option> + <option value="Glu-C">Glu-C</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Elastase">Elastase</option> + <option value="Thermolysin">Thermolysin</option> + <option value="No Enzyme">No Enzyme</option> + </param> + <param argument="-frag" type="select" optional="true" label="Fragmentation"> + <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option> + <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option> + <option value="ETD">ETD (C/Z/Z+1)</option> + </param> + </when> + </conditional> + </xml> + <xml name="encyclopedia_common_options"> + <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false" + token_cid_selected="true" token_hcd_selected="false"/> + </xml> + <xml name="walnut_common_options"> + <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" + token_cid_selected="false" token_hcd_selected="true"/> + </xml> + <token name="@COMMON_OPTIONS@"> + #if $acquisition.set_acquisition == 'yes' + -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched + #if $acquisition.acquisition + -acquisition '$acquisition.acquisition' + #end if + #if $acquisition.enzyme: + -enzyme '$acquisition.enzyme' + #end if + #if $acquisition.frag: + -frag '$acquisition.frag' + #end if + #end if + </token> + + <xml name="mass_tolerance"> + <conditional name="tolerance"> + <param name="set_tolerance" type="select" label="Set Tolerance Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <conditional name="precursor_tolerance"> + <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance"> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="PPM"> + <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/> + </when> + </conditional> + <conditional name="fragment_tolerance"> + <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance"> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="PPM"> + <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/> + </when> + </conditional> + <yield/> + </when> + </conditional> + </xml> + <token name="@MASS_TOLERANCE@"> + #if $tolerance.set_tolerance == 'yes' + -ptolunits $tolerance.precursor_tolerance.ptolunits + -ptol $tolerance.precursor_tolerance.ptol + -ftolunits $tolerance.fragment_tolerance.ftolunits + -ftol $tolerance.fragment_tolerance.ftol + #end if + </token> + + <xml name="mass_library_tolerance"> + <expand macro="mass_tolerance"> + <conditional name="library_tolerance"> + <param argument="-ltolunits" type="select" label="Library Mass Tolerance"> + <option value="defaults">Use defaults</option> + <option value="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <when value="defaults"/> + <when value="PPM"> + <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/> + </when> + <when value="AMU"> + <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/> + </when> + <when value="Resolution"> + <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/> + </when> + </conditional> + </expand> + </xml> + <token name="@MASS_LIBRARY_TOLERANCE@"> + @MASS_TOLERANCE@ + #if $tolerance.set_tolerance == 'yes' and $tolerance.library_tolerance.ltolunits != 'defaults' + -ltolunits $tolerance.library_tolerance.ltolunits + -ltol $tolerance.library_tolerance.ltol + #end if + </token> + + <xml name="percolator_options"> + <conditional name="percolator"> + <param name="set_percolator" type="select" label="Set Percolator Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> + <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> + <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> + </when> + </conditional> + </xml> + <token name="@PERCOLATOR_OPTIONS@"> + #if $percolator.set_percolator == 'yes' + #if str($percolator.percolatorVersionNumber) + -percolatorVersionNumber $percolator.percolatorVersionNumber + #end if + #if str($percolator.percolatorProteinThreshold) + -percolatorProteinThreshold $percolator.percolatorProteinThreshold + #end if + #if str($percolator.percolatorThreshold) + -percolatorThreshold $percolator.percolatorThreshold + #end if + #end if + </token> + + <xml name="peak_options"> + <conditional name="peak"> + <param name="set_peak" type="select" label="Set Peak Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/> + <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/> + <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/> + <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/> + <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/> + <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + </when> + </conditional> + </xml> + <token name="@PEAK_OPTIONS@"> + #if $peak.set_peak == 'yes' + #if str($peak.numberOfQuantitativePeaks) + -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks + #end if + #if str($peak.minNumOfQuantitativePeaks) + -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks + #end if + #if str($peak.minQuantitativeIonNumber) + -minQuantitativeIonNumber $peak.minQuantitativeIonNumber + #end if + #if str($peak.minIntensity) + -minIntensity $peak.minIntensity + #end if + #if str($peak.expectedPeakWidth) + -expectedPeakWidth $peak.expectedPeakWidth + #end if + #if $peak.filterPeaklists + -filterPeaklists $peak.filterPeaklists + #end if + #end if + </token> + + <xml name="window_options"> + <conditional name="window"> + <param name="set_window" type="select" label="Set Window Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/> + <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/> + <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/> + <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/> + <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/> + <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType"> + <option value="window">Across entire window</option> + <option value="recal20">Recalibrated (20% gradient)</option> + <option value="recal">Recalibrated (peak width only)</option> + <option value="uncal20">Uncalibrated (20% gradient)</option> + <option value="uncal">Uncalibrated (peak width only)</option> + </param> + </when> + </conditional> + </xml> + <token name="@WINDOW_OPTIONS@"> + #if $window.set_window == 'yes' + #if str($window.foffset) + -foffset $window.foffset + #end if + #if str($window.poffset) + -poffset $window.poffset + #end if + #if str($window.precursorIsolationMargin) + -precursorIsolationMargin $window.precursorIsolationMargin + #end if + #if str($window.precursorWindowSize) + -precursorWindowSize $window.precursorWindowSize + #end if + #if str($window.rtWindowInMin) + -rtWindowInMin $window.rtWindowInMin + #end if + #if $window.scoringBreadthType + -scoringBreadthType $window.scoringBreadthType + #end if + #end if + </token> + + <xml name="modification_options"> + <conditional name="modifications"> + <param name="set_modifications" type="select" label="Set Modifications Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-fixed" type="select" optional="true" label="Fixed Modification"> + <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option> + <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option> + <option value="C=45.987721">C+46 (MMTS) C=45.987721</option> + <option value="C=125.047679">C+125 (NEM) C=125.047679</option> + </param> + <yield/> + <!-- + <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> + </param> + --> + <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> + </when> + </conditional> + </xml> + <token name="@MODIFICATION_OPTIONS@"> + #if $modifications.set_modifications == 'yes' + #if $modifications.fixed + -fixed $modifications.fixed + #end if + -verifyModificationIons $modifications.verifyModificationIons + #end if + </token> + + <xml name="search_options"> + <conditional name="search"> + <param name="set_search" type="select" label="Set Search Options"> + <option value="no">No - use default options</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/> + <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/> + <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/> + <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/> + <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/> + <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> + <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> + <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> + <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> +<!-- + <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/> + <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/> + <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> + <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> +--> + </when> + </conditional> + </xml> + <token name="@SEARCH_OPTIONS@"> + #if $search.set_search == 'yes' + -minCharge $search.minCharge + -maxCharge $search.maxCharge + -minLength $search.minLength + -maxLength $search.maxLength + -minEluteTime $search.minEluteTime + -maxMissedCleavage $search.maxMissedCleavage + -minQuantitativeIonNumber $search.minQuantitativeIonNumber + -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks + -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks + ## -alpha $search.alpha + ## -beta $search.beta + ## -addDecoysToBackground $search.addDecoysToBackground + ## -dontRunDecoys $search.dontRunDecoys + #end if + </token> + <!-- +minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu + +acquisition (default: overlapping dia) + +addDecoysToBackground (default: false) + +alpha (default: 1.8) + +beta (default: 0.4) + +dontRunDecoys (default: false) + +enzyme (default: trypsin) + +filterPeaklists (default: false) + +fixed (default: C=57.0214635) + +foffset (default: 0) + =frag (default: YONLY) + +ftol (default: 10) + +ftolunits (default: ppm) + +maxCharge (default: 3) + +ftolunits (default: ppm) + +maxCharge (default: 3) + +maxLength (default: 100) + +maxMissedCleavage (default: 1) + +minCharge (default: 2) + +minEluteTime (default: 12) + +minIntensity (default: -1.0) + +minLength (default: 5) + +minNumOfQuantitativePeaks (default: 3) + +minQuantitativeIonNumber (default: 3) + +numberOfQuantitativePeaks (default: 5) + -numberOfReportedPeaks (default: 1) + -numberOfThreadsUsed (default: 12) + +percolatorProteinThreshol (default: 0.01) + +percolatorThreshold (default: 0.01) + +percolatorVersionNumber (default: 3) + +poffset (default: 0) + +precursorIsolationMargin (default: 0) + +precursorWindowSize (default: -1) + +ptol (default: 10) + +ptolunits (default: ppm) + -requireVariableMods (default: false) + -variable (default: -) + --> + <xml name="libexport"> + <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> + </xml> +</macros> +<!-- +e w t x l param ++:+:+:+:+ i ++:+:+:+:+ l ++:+:+:+:+ f + ++:+:+:+:+ t +-:+:-:+:- tp +-:+:-:+:+ a + ++:+:+:+:+ o + ++:+:+:+:- acquisition +-:+:-:+:- addDecoysToBackground +-:+:-:+:- alpha +-:+:-:+:- beta +-:-:-:-:+ blib +-:+:-:+:- dontRunDecoys ++:+:+:+:- enzyme ++:-:+:-:- expectedPeakWidth ++:+:+:+:- filterPeaklists ++:+:+:+:+ fixed ++:+:+:+:+ foffset ++:+:+:+:- frag ++:+:+:+:+ ftol ++:+:+:+:+ ftolunits ++:-:+:-:- lftol ++:-:+:-:- lftolunits ++:-:-:-:- libexport ++:-:+:-:+ localizationModification +-:+:-:+:- maxCharge +-:+:-:+:- maxLength +-:+:-:+:- maxMissedCleavage +-:+:-:+:- minCharge +-:+:-:+:- minEluteTime ++:+:+:+:- minIntensity +-:+:-:+:- minLength ++:+:+:+:+ minNumOfQuantitativePeaks ++:+:+:+:+ minQuantitativeIonNumber ++:-:+:-:+ numberOfExtraDecoyLibrariesSearched ++:+:+:+:+ numberOfQuantitativePeaks +-:+:-:+:- numberOfReportedPeaks +-:+:-:+:- numberOfThreadsUsed +-:-:-:-:+ percolatorLocation +-:+:-:+:- percolatorProteinThreshol ++:-:+:-:+ percolatorProteinThreshold ++:+:+:+:+ percolatorThreshold ++:+:+:+:- percolatorVersionNumber +-:-:-:-:+ phospho ++:+:+:+:- poffset ++:+:+:+:- precursorIsolationMargin ++:+:+:+:- precursorWindowSize ++:+:+:+:- ptol ++:+:+:+:- ptolunits +-:+:-:+:- requireVariableMods ++:-:+:-:- rtWindowInMin ++:-:+:-:- scoringBreadthType +-:+:-:+:- variable ++:-:+:-:- verifyModificationIons +-->