# HG changeset patch # User jjohnson # Date 1593617099 14400 # Node ID 114b44e35d3047d7b581d78385fd6d7c3c9cc50f # Parent 6635b68da94878adf15a3d771baa1054d9554f78 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f" diff -r 6635b68da948 -r 114b44e35d30 encyclopedia_walnut.xml --- a/encyclopedia_walnut.xml Tue Jun 30 11:42:28 2020 -0400 +++ b/encyclopedia_walnut.xml Wed Jul 01 11:24:59 2020 -0400 @@ -26,13 +26,7 @@ - - - - - - - + diff -r 6635b68da948 -r 114b44e35d30 macros.xml --- a/macros.xml Tue Jun 30 11:42:28 2020 -0400 +++ b/macros.xml Wed Jul 01 11:24:59 2020 -0400 @@ -1,28 +1,4 @@ - 0.9.5 @@ -30,6 +6,7 @@ + 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. @@ -43,6 +20,7 @@ + #import re #def identifier_or_name($input1) @@ -207,16 +185,16 @@ token_cid_selected="false" token_hcd_selected="true"/> - #if $acquisition.set_acquisition == 'yes' - -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched - #if $acquisition.acquisition - -acquisition '$acquisition.acquisition' + #if $options.acquisition.set_acquisition == 'yes' + -numberOfExtraDecoyLibrariesSearched $options.acquisition.numberOfExtraDecoyLibrariesSearched + #if $options.acquisition.acquisition + -acquisition '$options.acquisition.acquisition' #end if - #if $acquisition.enzyme: - -enzyme '$acquisition.enzyme' + #if $options.acquisition.enzyme: + -enzyme '$options.acquisition.enzyme' #end if - #if $acquisition.frag: - -frag '$acquisition.frag' + #if $options.acquisition.frag: + -frag '$options.acquisition.frag' #end if #end if @@ -266,11 +244,11 @@ - #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 + #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 @@ -298,9 +276,9 @@ @MASS_TOLERANCE@ - #if $tolerance.set_tolerance == 'yes' and $tolerance.library_tolerance.ltolunits != 'defaults' - -ltolunits $tolerance.library_tolerance.ltolunits - -ltol $tolerance.library_tolerance.ltol + #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 @@ -319,15 +297,15 @@ - #if $percolator.set_percolator == 'yes' - #if str($percolator.percolatorVersionNumber) - -percolatorVersionNumber $percolator.percolatorVersionNumber + #if $options.percolator.set_percolator == 'yes' + #if str($options.percolator.percolatorVersionNumber) + -percolatorVersionNumber $options.percolator.percolatorVersionNumber #end if - #if str($percolator.percolatorProteinThreshold) - -percolatorProteinThreshold $percolator.percolatorProteinThreshold + #if str($options.percolator.percolatorProteinThreshold) + -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold #end if - #if str($percolator.percolatorThreshold) - -percolatorThreshold $percolator.percolatorThreshold + #if str($options.percolator.percolatorThreshold) + -percolatorThreshold $options.percolator.percolatorThreshold #end if #end if @@ -353,24 +331,24 @@ - #if $peak.set_peak == 'yes' - #if str($peak.numberOfQuantitativePeaks) - -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks + #if $options.peak.set_peak == 'yes' + #if str($options.peak.numberOfQuantitativePeaks) + -numberOfQuantitativePeaks $options.peak.numberOfQuantitativePeaks #end if - #if str($peak.minNumOfQuantitativePeaks) - -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks + #if str($options.peak.minNumOfQuantitativePeaks) + -minNumOfQuantitativePeaks $options.peak.minNumOfQuantitativePeaks #end if - #if str($peak.minQuantitativeIonNumber) - -minQuantitativeIonNumber $peak.minQuantitativeIonNumber + #if str($options.peak.minQuantitativeIonNumber) + -minQuantitativeIonNumber $options.peak.minQuantitativeIonNumber #end if - #if str($peak.minIntensity) - -minIntensity $peak.minIntensity + #if str($options.peak.minIntensity) + -minIntensity $options.peak.minIntensity #end if - #if str($peak.expectedPeakWidth) - -expectedPeakWidth $peak.expectedPeakWidth + #if str($options.peak.expectedPeakWidth) + -expectedPeakWidth $options.peak.expectedPeakWidth #end if - #if $peak.filterPeaklists - -filterPeaklists $peak.filterPeaklists + #if $options.peak.filterPeaklists + -filterPeaklists $options.peak.filterPeaklists #end if #end if @@ -399,24 +377,24 @@ - #if $window.set_window == 'yes' - #if str($window.foffset) - -foffset $window.foffset + #if $options.window.set_window == 'yes' + #if str($options.window.foffset) + -foffset $options.window.foffset #end if - #if str($window.poffset) - -poffset $window.poffset + #if str($options.window.poffset) + -poffset $options.window.poffset #end if - #if str($window.precursorIsolationMargin) - -precursorIsolationMargin $window.precursorIsolationMargin + #if str($options.window.precursorIsolationMargin) + -precursorIsolationMargin $options.window.precursorIsolationMargin #end if - #if str($window.precursorWindowSize) - -precursorWindowSize $window.precursorWindowSize + #if str($options.window.precursorWindowSize) + -precursorWindowSize $options.window.precursorWindowSize #end if - #if str($window.rtWindowInMin) - -rtWindowInMin $window.rtWindowInMin + #if str($options.window.rtWindowInMin) + -rtWindowInMin $options.window.rtWindowInMin #end if - #if $window.scoringBreadthType - -scoringBreadthType $window.scoringBreadthType + #if $options.window.scoringBreadthType + -scoringBreadthType $options.window.scoringBreadthType #end if #end if @@ -445,11 +423,11 @@ - #if $modifications.set_modifications == 'yes' - #if $modifications.fixed - -fixed $modifications.fixed + #if $options.modifications.set_modifications == 'yes' + #if $options.modifications.fixed + -fixed $options.modifications.fixed #end if - -verifyModificationIons $modifications.verifyModificationIons + -verifyModificationIons $options.modifications.verifyModificationIons #end if @@ -471,8 +449,6 @@ @@ -480,22 +456,32 @@ - #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 + #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 + + +
+ + + + + + +
+
+ diff -r 6635b68da948 -r 114b44e35d30 static/images/SearchToLib_Workflow.png Binary file static/images/SearchToLib_Workflow.png has changed