#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
    
        
    #set $i_name = $ln_name($scan_input)
    ln -s '$scan_input' '$i_name' &&
    
        
    #set $f_name = $ln_name($fasta)
    ln -s '$fasta' '$f_name' &&
    
        
    #if $target_fasta
    #set $t_name = $ln_name($target_fasta)
    ln -s '$target_fasta' '$t_name' &&
    #else
    #set $t_name = None
    #end if
    
        EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -walnut
            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
        
    -i '$i_name'
    
        
    -f '$f_name'
    
        
    #if $t_name
    -t '$t_name'
    -tp $tp
    #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
    
    #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.percolatorVersion)
            -percolatorVersion $options.percolator.percolatorVersion
        #end if
        #if str($options.percolator.percolatorProteinThreshold)
            -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
        #end if
        #if str($options.percolator.percolatorThreshold)
            -percolatorThreshold $options.percolator.percolatorThreshold
        #end if
    #else 
        -percolatorVersion "3.01"
    #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
    
        -o gxpedia