Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.12.34+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/0.9.5.0 |
encyclopedia_quantify |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
encyclopedia | 1.12.34 | package |
Additional information about this tool |
#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 $inputs_dir = 'inputs' mkdir -p $inputs_dir && #for $sf in $scan_inputs #set $i_name = $ln_name($sf) ln -s '$sf' '${inputs_dir}/${i_name}' && #end for #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 #if $library #set $l_name = $ln_name($library) cp '$library' '$l_name' && #else #set $l_name = None #end if for SCAN_FILE in `ls -1 inputs/*`; do echo "\$SCAN_FILE" && EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" #if not $library -walnut #end if -i \$SCAN_FILE -f '$f_name' #if $t_name -t '$t_name' -tp $tp #end if #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 #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 | tee -a search2lib.log ; done && for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport #if not $library -pecan #end if -i '$inputs_dir' -f '$f_name' #if $t_name -t '$t_name' -tp $tp #end if #if $l_name -l '$l_name' #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 -a $a -o chromatogram_library.elib && ls -l ./*.* inputs/* | tee -a search2lib.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
scan_inputs: ['BCS_hela_wide_500_900_1.mzML', 'BCS_hela_wide_500_900_2.mzML'] library: BCS_hela.elib fasta: uniprot_human.fasta |
name: value name: value |
BCS_hela_wide_500_900_1.mzML BCS_hela_wide_500_900_2.mzML BCS_hela.elib uniprot_human.fasta value |