Mercurial > repos > jjohnson > encyclopedia_searchtolib
changeset 2:a74d446c8f5f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
| author | jjohnson |
|---|---|
| date | Wed, 01 Jul 2020 11:25:18 -0400 |
| parents | a7d52df6763f |
| children | 899fc684202e |
| files | encyclopedia_searchtolib.xml macros.xml static/images/SearchToLib_Workflow.png |
| diffstat | 3 files changed, 83 insertions(+), 103 deletions(-) [+] |
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--- a/encyclopedia_searchtolib.xml Tue Jun 30 11:43:03 2020 -0400 +++ b/encyclopedia_searchtolib.xml Wed Jul 01 11:25:18 2020 -0400 @@ -45,14 +45,8 @@ <expand macro="lib_input" optional="true" libhelp="Use a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/> <expand macro="fasta_input"/> <expand macro="target_fasta"/> - <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides is generally not needed when using narrow-window spectrums"/> - <expand macro="common_options"/> - <expand macro="mass_library_tolerance"/> - <expand macro="percolator_options"/> - <expand macro="peak_options"/> - <expand macro="window_options"/> - <expand macro="modification_options"/> - <expand macro="search_options"/> + <expand macro="options_section"/> + <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides is generally not needed when when building a library from narrow-window spectrums"/> <param name="select_outputs" type="select" label="Select outputs" multiple="true"> <option value="log" selected="true">log</option> <option value="elib" selected="true">elib</option> @@ -132,8 +126,8 @@ 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library to produce quantification results. .. image:: SearchToLib_Workflow.png - :height: 439 - :width: 768 + :width: 810 + :height: 580 .. _Prosit: https://www.proteomicsdb.org/prosit
--- a/macros.xml Tue Jun 30 11:43:03 2020 -0400 +++ b/macros.xml Wed Jul 01 11:25:18 2020 -0400 @@ -1,28 +1,4 @@ <macros> -<!-- -# generate a Walnut CLIB from GPF-DIA and a FASTA -for i in library/*.mzML; do - java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -walnut -i $i -f uniprot_yeast_25jan2019.fasta; -done -java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -walnut -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; - -# process single-injection DIA with the CLIB -for i in quant/*.mzML; do - java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; -done - -Next for Prosit: -# generate an EncyclopeDIA CLIB from GPF-DIA and a Prosit Library -for i in library/*.mzML; do - java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l prosit_library.dlib -f uniprot_yeast_25jan2019.fasta; -done -java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -libexport -o chromatogram_library.elib -i library -f uniprot_yeast_25jan2019.fasta -a false; - -# process single-injection DIA with the CLIB (exactly the same as with Walnut) -for i in quant/*.mzML; do - java -Xmx20g -jar encyclopedia-0.9.0-executable.jar -i $i -l chromatogram_library.elib -f uniprot_yeast_25jan2019.fasta; -done ---> <token name="@VERSION@">0.9.5</token> <xml name="requirements"> <requirements> @@ -30,6 +6,7 @@ <yield/> </requirements> </xml> + <token name="@ENCYCLOPEDIA_WIKI@"> EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. @@ -43,6 +20,7 @@ <yield/> </citations> </xml> + <token name="@CMD_IMPORTS@"> #import re #def identifier_or_name($input1) @@ -207,16 +185,16 @@ token_cid_selected="false" token_hcd_selected="true"/> </xml> <token name="@COMMON_OPTIONS@"> - #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 </token> @@ -266,11 +244,11 @@ </conditional> </xml> <token name="@MASS_TOLERANCE@"> - #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 </token> @@ -298,9 +276,9 @@ </xml> <token name="@MASS_LIBRARY_TOLERANCE@"> @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 </token> @@ -319,15 +297,15 @@ </conditional> </xml> <token name="@PERCOLATOR_OPTIONS@"> - #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 </token> @@ -353,24 +331,24 @@ </conditional> </xml> <token name="@PEAK_OPTIONS@"> - #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 </token> @@ -399,24 +377,24 @@ </conditional> </xml> <token name="@WINDOW_OPTIONS@"> - #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 </token> @@ -445,11 +423,11 @@ </conditional> </xml> <token name="@MODIFICATION_OPTIONS@"> - #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 </token> @@ -471,8 +449,6 @@ <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/> <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/> <!-- - <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/> - <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/> <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> --> @@ -480,22 +456,32 @@ </conditional> </xml> <token name="@SEARCH_OPTIONS@"> - #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 </token> + + <xml name="options_section"> + <section name="options" title="Parameter Settings" expanded="false"> + <expand macro="common_options"/> + <expand macro="mass_library_tolerance"/> + <expand macro="percolator_options"/> + <expand macro="peak_options"/> + <expand macro="window_options"/> + <expand macro="modification_options"/> + </section> + </xml> + <xml name="libexport"> <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> </xml>