Mercurial > repos > galaxyp > encyclopedia_quantify
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34
author | galaxyp |
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date | Tue, 17 May 2022 14:55:35 +0000 |
parents | 1c5cbf8f79ce |
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<macros> <token name="@TOOL_VERSION@">1.12.34</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement> <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. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home .. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home </token> <xml name="citations"> <citations> <citation type="doi">10.1038/s41467-018-07454-w</citation> <citation type="doi">10.1038/s41467-020-15346-1</citation> <citation type="doi">10.1074/mcp.P119.001913</citation> <yield/> </citations> </xml> <token name="@CMD_IMPORTS@"> #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 </token> <xml name="scan_input"> <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> <help>@MSCONVERT_RAW@</help> </param> </xml> <token name="@LINK_SCAN_INPUT@"><![CDATA[ #set $i_name = $ln_name($scan_input) ln -s '$scan_input' '$i_name' && ]]></token> <token name="@SCAN_INPUT@"> -i '$i_name' </token> <xml name="scan_inputs"> <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> <help>@MSCONVERT_RAW@</help> </param> </xml> <token name="@LINK_SCAN_INPUTS@"><![CDATA[ #set $inputs_dir = 'inputs' mkdir -p $inputs_dir && #for $sf in $scan_inputs #set $i_name = $ln_name($sf) ln -s '$sf' '${inputs_dir}/${i_name}' && #end for ]]></token> <token name="@SCAN_INPUTS@"> -i '$inputs_dir' </token> <xml name="fasta_input"> <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> </param> </xml> <token name="@LINK_FASTA_INPUT@"><![CDATA[ #set $f_name = $ln_name($fasta) ln -s '$fasta' '$f_name' && ]]></token> <token name="@FASTA_INPUT@"> -f '$f_name' </token> <xml name="target_fasta"> <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> <help>Optional - Only analyze this subset of the background fasta proteome</help> </param> <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides"> <help>Rather than full proteins</help> </param> </xml> <token name="@LINK_TARGET_FASTA@"><![CDATA[ #if $target_fasta #set $t_name = $ln_name($target_fasta) ln -s '$target_fasta' '$t_name' && #else #set $t_name = None #end if ]]></token> <token name="@TARGET_FASTA@"> #if $t_name -t '$t_name' -tp $tp #end if </token> <xml name="lib_input" token_optional="true" token_libhelp=""> <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> <help>@LIBHELP@</help> </param> </xml> <token name="@LINK_LIB_INPUT@"><![CDATA[ #if $library #set $l_name = $ln_name($library) cp '$library' '$l_name' && #else #set $l_name = None #end if ]]></token> <token name="@LIB_INPUT@"> #if $l_name -l '$l_name' #end if </token> <xml name="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="false" token_cid_selected="false" token_hcd_selected="false"> <conditional name="acquisition"> <param name="set_acquisition" type="select" label="Set Acquisition Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> <param argument="-acquisition" type="select" optional="true" label="Data Acquization Type"> <option value="Overlapping DIA" selected="@OVERLAPPING_SELECTED@">Overlapping DIA</option> <option value="Non-Overlapping DIA" selected="@NONOVERLAPPING_SELECTED@">Non-Overlapping DIA</option> </param> <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme"> <option value="Trypsin">Trypsin</option> <option value="Trypsin/p">Trypsin/p</option> <option value="Lys-C">Lys-C</option> <option value="Lys-N">Lys-N</option> <option value="Arg-C">Arg-C</option> <option value="Glu-C">Glu-C</option> <option value="Chymotrypsin">Chymotrypsin</option> <option value="Pepsin A">Pepsin A</option> <option value="Elastase">Elastase</option> <option value="Thermolysin">Thermolysin</option> <option value="No Enzyme">No Enzyme</option> </param> <param argument="-frag" type="select" optional="true" label="Fragmentation"> <option value="CID" selected="@CID_SELECTED@">CID/HCD (B/Y)</option> <option value="HCD" selected="@HCD_SELECTED@">HCD (Y-Only)</option> <option value="ETD">ETD (C/Z/Z+1)</option> </param> </when> </conditional> </xml> <xml name="encyclopedia_common_options"> <expand macro="common_options" token_overlapping_selected="true" token_nonoverlapping_selected="false" token_cid_selected="true" token_hcd_selected="false"/> </xml> <xml name="walnut_common_options"> <expand macro="common_options" token_overlapping_selected="false" token_nonoverlapping_selected="true" token_cid_selected="false" token_hcd_selected="true"/> </xml> <token name="@COMMON_OPTIONS@"> #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 </token> <xml name="mass_tolerance"> <conditional name="tolerance"> <param name="set_tolerance" type="select" label="Set Tolerance Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <conditional name="precursor_tolerance"> <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance"> <option value="PPM">PPM</option> <option value="AMU">AMU</option> <option value="Resolution">Resolution</option> </param> <when value="PPM"> <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/> </when> <when value="AMU"> <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/> </when> <when value="Resolution"> <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/> </when> </conditional> <conditional name="fragment_tolerance"> <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance"> <option value="PPM">PPM</option> <option value="AMU">AMU</option> <option value="Resolution">Resolution</option> </param> <when value="PPM"> <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/> </when> <when value="AMU"> <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/> </when> <when value="Resolution"> <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/> </when> </conditional> <yield/> </when> </conditional> </xml> <token name="@MASS_TOLERANCE@"> #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> <xml name="mass_library_tolerance"> <expand macro="mass_tolerance"> <conditional name="library_tolerance"> <param argument="-ltolunits" type="select" label="Library Mass Tolerance"> <option value="defaults">Use defaults</option> <option value="PPM">PPM</option> <option value="AMU">AMU</option> <option value="Resolution">Resolution</option> </param> <when value="defaults"/> <when value="PPM"> <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/> </when> <when value="AMU"> <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/> </when> <when value="Resolution"> <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/> </when> </conditional> </expand> </xml> <token name="@MASS_LIBRARY_TOLERANCE@"> @MASS_TOLERANCE@ #if $options.tolerance.set_tolerance == 'yes' and $options.tolerance.library_tolerance.ltolunits != 'defaults' -ltolunits $options.tolerance.library_tolerance.ltolunits -ltol $options.tolerance.library_tolerance.ltol #end if </token> <xml name="percolator_options"> <conditional name="percolator"> <param name="set_percolator" type="select" label="Set Percolator Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-percolatorVersion" type="text" value="3.01" optional="true" label="percolatorVersion"> <option value="2.10">2.10</option> <option value="3.01">3.01</option> <option value="3.05">3.05</option> <validator type="regex" message="Not percolator version format">^\d([.]\d+)?$</validator> </param> <param argument="-percolatorProteinThreshold" type="float" value="0.01" optional="true" label="percolatorProteinThreshold"/> <param argument="-percolatorThreshold" type="float" value="0.01" optional="true" label="percolatorThreshold"/> </when> </conditional> </xml> <token name="@PERCOLATOR_OPTIONS@"> #if $options.percolator.set_percolator == 'yes' #if str($options.percolator.percolatorVersion) -percolatorVersion $options.percolator.percolatorVersion #end if #if str($options.percolator.percolatorProteinThreshold) -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold #end if #if str($options.percolator.percolatorThreshold) -percolatorThreshold $options.percolator.percolatorThreshold #end if #else -percolatorVersion "3.01" #end if </token> <xml name="peak_options"> <conditional name="peak"> <param name="set_peak" type="select" label="Set Peak Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-numberOfQuantitativePeaks" type="integer" value="" min="1" max="100" optional="true" label="Number of Quantitative Peaks" help="(default 5)"/> <param argument="-minNumOfQuantitativePeaks" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Peaks" help="(default 3)"/> <param argument="-minQuantitativeIonNumber" type="integer" value="" min="0" max="100" optional="true" label="Minimum Number of Quantitative Ions" help="(default 3)"/> <param argument="-minIntensity" type="float" value="-1.0" optional="true" label="minIntensity"/> <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" optional="true" label="Expected Peak Width" help="(default 5)"/> <param argument="-filterPeaklists" type="select" optional="true" label="Filter Peak Lists"> <option value="false">No</option> <option value="true">Yes</option> </param> </when> </conditional> </xml> <token name="@PEAK_OPTIONS@"> #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 </token> <xml name="window_options"> <conditional name="window"> <param name="set_window" type="select" label="Set Window Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-foffset" type="integer" value="" optional="true" label="fragmentOffsetPPM"/> <param argument="-poffset" type="integer" value="" optional="true" label="Precursor Offset PPM" help="-poffset"/> <param argument="-precursorIsolationMargin" type="integer" value="" optional="true" label="precursorIsolationMargin"/> <param argument="-precursorWindowSize" type="integer" value="" optional="true" label="precursorWindowSize"/> <param argument="-rtWindowInMin" type="float" value="" optional="true" label="rtWindowInMin"/> <param argument="-scoringBreadthType" type="select" optional="true" label="scoringBreadthType"> <option value="window">Across entire window</option> <option value="recal20">Recalibrated (20% gradient)</option> <option value="recal">Recalibrated (peak width only)</option> <option value="uncal20">Uncalibrated (20% gradient)</option> <option value="uncal">Uncalibrated (peak width only)</option> </param> </when> </conditional> </xml> <token name="@WINDOW_OPTIONS@"> #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 </token> <xml name="modification_options"> <conditional name="modifications"> <param name="set_modifications" type="select" label="Set Modifications Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-fixed" type="select" optional="true" label="Fixed Modification"> <option value="C=57.0214635">C+57 (Carbamidomethyl) C=57.0214635</option> <option value="C=58.005479">C+58 (Carboxymethyl) C=58.005479</option> <option value="C=45.987721">C+46 (MMTS) C=45.987721</option> <option value="C=125.047679">C+125 (NEM) C=125.047679</option> </param> <yield/> <!-- <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> </param> --> <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> </when> </conditional> </xml> <token name="@MODIFICATION_OPTIONS@"> #if $options.modifications.set_modifications == 'yes' #if $options.modifications.fixed -fixed $options.modifications.fixed #end if -verifyModificationIons $options.modifications.verifyModificationIons #end if </token> <xml name="search_options"> <conditional name="search"> <param name="set_search" type="select" label="Set Search Options"> <option value="no">No - use default options</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/> <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/> <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/> <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/> <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/> <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/> <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/> <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="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/> <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/> --> </when> </conditional> </xml> <token name="@SEARCH_OPTIONS@"> #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"/> <expand macro="search_options"/> </section> </xml> <xml name="libexport"> <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/> </xml> <token name="@SEARCH2LIB_CMDS@"><![CDATA[ @CMD_IMPORTS@ @LINK_SCAN_INPUTS@ @LINK_FASTA_INPUT@ @LINK_TARGET_FASTA@ @LINK_LIB_INPUT@ for SCAN_FILE in `ls -1 inputs/*`; do echo "\$SCAN_FILE" && EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" #if not $library -walnut #end if -i \$SCAN_FILE @FASTA_INPUT@ @TARGET_FASTA@ @LIB_INPUT@ @COMMON_OPTIONS@ @MASS_LIBRARY_TOLERANCE@ @PERCOLATOR_OPTIONS@ @PEAK_OPTIONS@ @WINDOW_OPTIONS@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ | tee -a search2lib.log ; done && for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport #if not $library -pecan #end if @SCAN_INPUTS@ @FASTA_INPUT@ @TARGET_FASTA@ @LIB_INPUT@ @MASS_LIBRARY_TOLERANCE@ @PERCOLATOR_OPTIONS@ @PEAK_OPTIONS@ @WINDOW_OPTIONS@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ -a $a -o chromatogram_library.elib && ls -l ./*.* inputs/* | tee -a search2lib.log ]]> </token> <token name="@MSCONVERT_CMD@"><![CDATA[ msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw ]]> </token> <token name="@MSCONVERT_RAW@"><![CDATA[ mzML conversion from RAW requires special options: @MSCONVERT_CMD@ ]]> </token> <token name="@MSCONVERT_HELP@"><![CDATA[ The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options: :: @MSCONVERT_CMD@ ]]> </token> </macros>