0.9.5
encyclopedia
EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home
.. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home
10.1038/s41467-018-07454-w
10.1038/s41467-020-15346-1
10.1074/mcp.P119.001913
#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'))))
#return $name_clean
#end def
#def ln_name($ds)
#set $ext = ''
#if $ds.is_of_type('mzml') or $ds.is_of_type('imzml')
#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 $t_name = None
@MSCONVERT_RAW@
-i '$i_name'
@MSCONVERT_RAW@
-i '$inputs_dir'
provides the necessary peptide-to-protein links not specified in the spectrum library
-f '$f_name'
Optional - Only analyze this subset of the background fasta proteome
Rather than full proteins
#if $t_name
-t '$t_name'
-tp $tp
#end if
@LIBHELP@
#if $l_name
-l '$l_name'
#end if
#if $options.acquisition.set_acquisition == 'yes'
-numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched
#if $options.acquisition.acquisition
-acquisition '$options.acquisition.acquisition'
#end if
#if $options.acquisition.enzyme:
-enzyme '$options.acquisition.enzyme'
#end if
#if $options.acquisition.frag:
-frag '$options.acquisition.frag'
#end if
#end if
#if $options.tolerance.set_tolerance == 'yes'
-ptolunits $options.tolerance.precursor_tolerance.ptolunits
-ptol $options.tolerance.precursor_tolerance.ptol
-ftolunits $options.tolerance.fragment_tolerance.ftolunits
-ftol $options.tolerance.fragment_tolerance.ftol
#end if
@MASS_TOLERANCE@
#if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults'
-ltolunits $options.tolerance.library_tolerance.ltolunits
-ltol $options.tolerance.library_tolerance.ltol
#end if
#if $options.percolator.set_percolator == 'yes'
#if str($options.percolator.percolatorVersionNumber)
-percolatorVersionNumber $options.percolator.percolatorVersionNumber
#end if
#if str($options.percolator.percolatorProteinThreshold)
-percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
#end if
#if str($options.percolator.percolatorThreshold)
-percolatorThreshold $options.percolator.percolatorThreshold
#end if
#end if
#if $options.peak.set_peak == 'yes'
#if str($options.peak.numberOfQuantitativePeaks)
-numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks
#end if
#if str($options.peak.minNumOfQuantitativePeaks)
-minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks
#end if
#if str($options.peak.minQuantitativeIonNumber)
-minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber
#end if
#if str($options.peak.minIntensity)
-minIntensity $options.peak.minIntensity
#end if
#if str($options.peak.expectedPeakWidth)
-expectedPeakWidth $options.peak.expectedPeakWidth
#end if
#if $options.peak.filterPeaklists
-filterPeaklists $options.peak.filterPeaklists
#end if
#end if
#if $options.window.set_window == 'yes'
#if str($options.window.foffset)
-foffset $options.window.foffset
#end if
#if str($options.window.poffset)
-poffset $options.window.poffset
#end if
#if str($options.window.precursorIsolationMargin)
-precursorIsolationMargin $options.window.precursorIsolationMargin
#end if
#if str($options.window.precursorWindowSize)
-precursorWindowSize $options.window.precursorWindowSize
#end if
#if str($options.window.rtWindowInMin)
-rtWindowInMin $options.window.rtWindowInMin
#end if
#if $options.window.scoringBreadthType
-scoringBreadthType $options.window.scoringBreadthType
#end if
#end if
#if $options.modifications.set_modifications == 'yes'
#if $options.modifications.fixed
-fixed $options.modifications.fixed
#end if
-verifyModificationIons $options.modifications.verifyModificationIons
#end if
#if $options.search.set_search == 'yes'
-minCharge $options.search.minCharge
-maxCharge $options.search.maxCharge
-minLength $options.search.minLength
-maxLength $options.search.maxLength
-minEluteTime $options.search.minEluteTime
-maxMissedCleavage $options.search.maxMissedCleavage
-minQuantitativeIonNumber $options.search.minQuantitativeIonNumber
-minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks
-numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks
## -addDecoysToBackground $options.search.addDecoysToBackground
## -dontRunDecoys $options.search.dontRunDecoys
#end if