# HG changeset patch
# User galaxyp
# Date 1568985404 14400
# Node ID 39618cb4669fa83efc557c57238a6eda27589ca5
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
diff -r 000000000000 -r 39618cb4669f encyclopedia.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia.xml Fri Sep 20 09:16:44 2019 -0400
@@ -0,0 +1,140 @@
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+ Mass Spec DIA data analysis
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+ macros.xml
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+ 'log' in select_outputs
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+ 'elib' in select_outputs
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+ 'first_delta_rt_pdf' in select_outputs
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+ 'first_rt_fit_pdf' in select_outputs
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+ 'first_rt_fit_txt' in select_outputs
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+ 'final_delta_rt_pdf' in select_outputs
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+ 'final_rt_fit_pdf' in select_outputs
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+ 'final_rt_fit_txt' in select_outputs
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+ 'features' in select_outputs
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+ 'encyclopedia' in select_outputs
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+ 'encyclopedia_decoy' in select_outputs
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diff -r 000000000000 -r 39618cb4669f macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Sep 20 09:16:44 2019 -0400
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+ 0.9.0
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+ encyclopedia
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+ #import re
+ #set $i_name = None
+ #set $f_name = None
+ #set $l_name = None
+ #set $t_name = None
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+
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+ -i '$i_name'
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+ -i '$inputs_dir'
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+ -f '$f_name'
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+ #if $t_name
+ -t '$t_name'
+ -tp $tp
+ #end if
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+ -l '$l_name'
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+ -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched
+ -acquisition '$acquisition.acquisition'
+ -enzyme '$acquisition.enzyme'
+ -frag '$acquisition.frag'
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+ -ptolunits $tolerance.precursor_tolerance.ptolunits
+ -ptol $tolerance.precursor_tolerance.ptol
+ -ftolunits $tolerance.fragment_tolerance.ftolunits
+ -ftol $tolerance.fragment_tolerance.ftol
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+ @MASS_TOLERANCE@
+ -ltolunits $tolerance.library_tolerance.ltolunits
+ -ltol $tolerance.library_tolerance.ltol
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+
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+
+
+
+ #if str($percolator.percolatorVersionNumber)
+ -percolatorVersionNumber $percolator.percolatorVersionNumber
+ #end if
+ #if str($percolator.percolatorProteinThreshold)
+ -percolatorProteinThreshold $percolator.percolatorProteinThreshold
+ #end if
+ #if str($percolator.percolatorThreshold)
+ -percolatorThreshold $percolator.percolatorThreshold
+ #end if
+
+
+
+
+
+
+ #if str($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
+ -filterPeaklists $peak.filterPeaklists
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+ -foffset $window.foffset
+ -poffset $window.poffset
+ -precursorIsolationMargin $window.precursorIsolationMargin
+ -precursorWindowSize $window.precursorWindowSize
+ -rtWindowInMin $window.rtWindowInMin
+ -scoringBreadthType $window.scoringBreadthType
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+ -verifyModificationIons $modifications.verifyModificationIons
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+ -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
+
+minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
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diff -r 000000000000 -r 39618cb4669f searchtolib.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/searchtolib.xml Fri Sep 20 09:16:44 2019 -0400
@@ -0,0 +1,155 @@
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+ PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data
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+ macros.xml
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+ 'log' in select_outputs
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+ 'elib' in select_outputs
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+ 'features' in select_outputs
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+ 'results' in select_outputs
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+ 'decoy' in select_outputs
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+ 'peptides' in select_outputs
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+ 'proteins' in select_outputs
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diff -r 000000000000 -r 39618cb4669f walnut.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/walnut.xml Fri Sep 20 09:16:44 2019 -0400
@@ -0,0 +1,119 @@
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+ PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data
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+ macros.xml
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+ 'log' in select_outputs
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+ 'elib' in select_outputs
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+ 'features' in select_outputs
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+ 'pecan' in select_outputs
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+ 'pecan_decoy' in select_outputs
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