# HG changeset patch # User galaxyp # Date 1600103166 0 # Node ID 4081e4faa4ab64b0932a7543b08399b95d9d063b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97" diff -r 000000000000 -r 4081e4faa4ab encyclopedia_quantify.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_quantify.xml Mon Sep 14 17:06:06 2020 +0000 @@ -0,0 +1,147 @@ + + samples from Data-Independent Acquisition (DIA) MS/MS Data + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + 'log' in select_outputs + + + 'elib' in select_outputs + + + 'features' in select_outputs + + + + + + 'results' in select_outputs + + + + + + 'decoy' in select_outputs + + + + + + library and 'rt_plots' in select_outputs + + + + library and 'rt_tables' in select_outputs + + + + a and 'peptides' in select_outputs + + + + + + a and 'proteins' in select_outputs + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 4081e4faa4ab macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 14 17:06:06 2020 +0000 @@ -0,0 +1,551 @@ + + 0.9.5 + + + encyclopedia + + + + + +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' + + + + + @MSCONVERT_RAW@ + + + + + -i '$inputs_dir' + + + + + provides the necessary peptide-to-protein links not specified in the spectrum library + + + + + -f '$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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + + + @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 + + + + + + + + + + + + + + + + + + #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 + + + + + + + + + + + + + + + + + + + + + + + + #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 + + + +
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diff -r 000000000000 -r 4081e4faa4ab static/images/SearchToLib_Workflow.png Binary file static/images/SearchToLib_Workflow.png has changed