# HG changeset patch
# User galaxyp
# Date 1600103151 0
# Node ID ca7a315fb90231b286fa54beab2dc8243c4a544c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
diff -r 000000000000 -r ca7a315fb902 encyclopedia_fasta_to_prosit_csv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia_fasta_to_prosit_csv.xml Mon Sep 14 17:05:51 2020 +0000
@@ -0,0 +1,62 @@
+
+ Create Prosit CSV Input From a Protein FASTA
+
+ macros.xml
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diff -r 000000000000 -r ca7a315fb902 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Sep 14 17:05:51 2020 +0000
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+
+ 0.9.5
+
+
+ encyclopedia
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+
+
+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'
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+
+
+
+ @MSCONVERT_RAW@
+
+
+
+
+ -i '$inputs_dir'
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+
+
+
+ provides the necessary peptide-to-protein links not specified in the spectrum library
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+
+
+
+ -f '$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
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+ #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
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+
+ #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
+
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+ @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
+
+
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+
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+
+
+ #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
+
+
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+
+ #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
+
+
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+ #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
+
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+ #if $options.modifications.set_modifications == 'yes'
+ #if $options.modifications.fixed
+ -fixed $options.modifications.fixed
+ #end if
+ -verifyModificationIons $options.modifications.verifyModificationIons
+ #end if
+
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+ #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
+
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diff -r 000000000000 -r ca7a315fb902 static/images/SearchToLib_Workflow.png
Binary file static/images/SearchToLib_Workflow.png has changed