Mercurial > repos > jjohnson > encyclopedia_prosit_csv_to_library
view macros.xml @ 0:75d11473e378 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 10:20:35 -0400 |
| parents | |
| children | 4887392414f1 |
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<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 -->