Mercurial > repos > galaxyp > encyclopedia
changeset 0:39618cb4669f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 557e4cb7a26bdce09a6666d0f59de5734be5995f
| author | galaxyp |
|---|---|
| date | Fri, 20 Sep 2019 09:16:44 -0400 |
| parents | |
| children | 8f2555d3687f |
| files | encyclopedia.xml macros.xml searchtolib.xml walnut.xml |
| diffstat | 4 files changed, 828 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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 @@ +<tool id="encyclopedia" name="EncyclopeDIA" version="@VERSION@.0"> + <description>Mass Spec DIA data analysis</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + @CMD_IMPORTS@ + @LINK_SCAN_INPUT@ + @LINK_FASTA_INPUT@ + @LINK_LIB_INPUT@ + EncyclopeDIA -Djava.awt.headless=true + @SCAN_INPUT@ + @FASTA_INPUT@ + @LIB_INPUT@ + @COMMON_OPTIONS@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + -o gxpedia + ]]></command> + <inputs> + <expand macro="scan_input"/> + <expand macro="fasta_input"/> + <expand macro="lib_input"/> + <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"/> + <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> + <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option> + <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option> + <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option> + <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option> + <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option> + <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option> + <option value="features" selected="true">features.txt</option> + <option value="encyclopedia" selected="true">encyclopedia.txt</option> + <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> + <filter>'log' in select_outputs</filter> + </data> + <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib"> + <filter>'elib' in select_outputs</filter> + </data> + <data name="first_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.delta_rt.pdf"> + <filter>'first_delta_rt_pdf' in select_outputs</filter> + </data> + <data name="first_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.pdf"> + <filter>'first_rt_fit_pdf' in select_outputs</filter> + </data> + <data name="first_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.txt"> + <filter>'first_rt_fit_txt' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" /> + </actions> + </data> + <data name="final_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.delta_rt.pdf"> + <filter>'final_delta_rt_pdf' in select_outputs</filter> + </data> + <data name="final_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.pdf"> + <filter>'final_rt_fit_pdf' in select_outputs</filter> + </data> + <data name="final_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.txt"> + <filter>'final_rt_fit_txt' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" /> + </actions> + </data> + <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt"> + <filter>'features' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,deltaCN,primary,xCorrLib,xCorrModel,LogDotProduct,logWeightedDotProduct,sumOfSquaredErrors,weightedSumOfSquaredErrors,numberOfMatchingPeaks,numberOfMatchingPeaksAboveThreshold,averageAbsFragmentDeltaMass,averageFragmentDeltaMasses,isotopeDotProduct,averageAbsParentDeltaMass,averageParentDeltaMass,eValue,deltaRT,pepLength,charge2,charge3,precursorMz,RTinMin,sequence,protein" /> + </actions> + </data> + <data name="encyclopedia" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt" from_work_dir="gxpedia.encyclopedia.txt"> + <filter>'encyclopedia' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <data name="encyclopedia_decoy" format="tabular" label="${tool.name} ${on_string} encyclopedia.decoy.txt" from_work_dir="gxpedia.encyclopedia.decoy.txt"> + <filter>'encyclopedia_decoy' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + </outputs> + <help><![CDATA[ +EncyclopeDIA is a library search engine for DIA data. +You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb + +Required Parameters: + -i input .DIA or .MZML file + -f protein .FASTA database + -l library .ELIB file + +Other Parameters: + -o output report file (default: [input file].encyclopedia.txt) + -acquisition (default: Non-Overlapping DIA) + -enzyme (default: trypsin) + -expectedPeakWidth (default: 25) + -filterPeaklists (default: false) + -fixed (default: C=57.0214635) + -foffset (default: 0) + -frag (default: CID) + -ftol (default: 10) + -ftolunits (default: ppm) + -lftol (default: 10) + -lftolunits (default: ppm) + -localizationModification (default: none) + -minIntensity (default: -1.0) + -minNumOfQuantitativePeaks (default: 3) + -minQuantitativeIonNumber (default: 3) + -numberOfExtraDecoyLibrariesSearched (default: 0.0) + -numberOfQuantitativePeaks (default: 5) + -percolatorProteinThreshold (default: 0.01) + -percolatorThreshold (default: 0.01) + -percolatorVersionNumber (default: 3) + -poffset (default: 0) + -precursorIsolationMargin (default: 0) + -precursorWindowSize (default: -1) + -ptol (default: 10) + -ptolunits (default: ppm) + -rtWindowInMin (default: -1.0) + -scoringBreadthType (default: window) + -verifyModificationIons (default: true) + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 20 09:16:44 2019 -0400 @@ -0,0 +1,414 @@ +<macros> + <token name="@VERSION@">0.9.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">encyclopedia</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> + <token name="@CMD_IMPORTS@"> + #import re + #set $i_name = None + #set $f_name = None + #set $l_name = None + #set $t_name = None + </token> + + <xml name="scan_input"> + <param argument="-i" type="data" format="mzml" label="Spectrum file, .mzml or .dia"/> + </xml> + <token name="@LINK_SCAN_INPUT@"><![CDATA[ + #set $i_name = $i.display_name + ln -s '$i' '$i_name' && + ]]></token> + <token name="@SCAN_INPUT@"> + -i '$i_name' + </token> + + <xml name="scan_inputs"> + <param argument="-i" type="data" format="mzml" multiple="true" label="Spectrum file, .mzml or .dia"/> + </xml> + <token name="@LINK_SCAN_INPUTS@"><![CDATA[ + #set $inputs_dir = 'inputs' + mkdir -p $inputs_dir && + #for $sf in $i + #set $i_name = $sf.display_name + ln -s '$sf' '${inputs_dir}/${i_name}' && + #end for + ]]></token> + <token name="@SCAN_INPUTS@"> + -i '$inputs_dir' + </token> + + <xml name="fasta_input"> + <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/> + </xml> + <token name="@LINK_FASTA_INPUT@"><![CDATA[ + #set $f_name = $f.display_name + ln -s '$f' '$f_name' && + ]]></token> + <token name="@FASTA_INPUT@"> + -f '$f_name' + </token> + + <xml name="target_fasta"> + <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/> + <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> + </xml> + <token name="@LINK_TARGET_FASTA@"><![CDATA[ + #if $t + #set $t_name = $t.display_name + ln -s '$t' '$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"> + <param argument="-l" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/> + </xml> + <token name="@LINK_LIB_INPUT@"><![CDATA[ + #set $l_name = $l.display_name + cp '$l' $l_name && + ]]></token> + <token name="@LIB_INPUT@"> + -l '$l_name' + </token> + + <xml name="common_options"> + <section name="acquisition" expanded="true" title="Acquisition Options"> + <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/> + <param argument="-acquisition" type="select" label="Data Acquization Type"> + <option value="Non-Overlapping DIA">Non-Overlapping DIA</option> + <option value="Overlapping DIA">Overlapping DIA</option> + </param> + <param argument="-enzyme" type="select" 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" label="Fragmentation"> + <option value="CID">CID/HCD (B/Y)</option> + <option value="HCD">HCD (Y-Only)</option> + <option value="ETD">ETD (C/Z/Z+1)</option> + </param> + </section> + </xml> + <token name="@COMMON_OPTIONS@"> + -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched + -acquisition '$acquisition.acquisition' + -enzyme '$acquisition.enzyme' + -frag '$acquisition.frag' + </token> + + <xml name="mass_tolerance"> + <section name="tolerance" expanded="true" title="Tolerance Options"> + <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/> + </section> + </xml> + <token name="@MASS_TOLERANCE@"> + -ptolunits $tolerance.precursor_tolerance.ptolunits + -ptol $tolerance.precursor_tolerance.ptol + -ftolunits $tolerance.fragment_tolerance.ftolunits + -ftol $tolerance.fragment_tolerance.ftol + </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="PPM">PPM</option> + <option value="AMU">AMU</option> + <option value="Resolution">Resolution</option> + </param> + <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@ + -ltolunits $tolerance.library_tolerance.ltolunits + -ltol $tolerance.library_tolerance.ltol + </token> + + <xml name="percolator_options"> + <section name="percolator" expanded="false" title="Pecolator Options"> + <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> + <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> + <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> + </section> + </xml> + <token name="@PERCOLATOR_OPTIONS@"> + #if str($percolator.percolatorVersionNumber) + -percolatorVersionNumber $percolator.percolatorVersionNumber + #end if + #if str($percolator.percolatorProteinThreshold) + -percolatorProteinThreshold $percolator.percolatorProteinThreshold + #end if + #if str($percolator.percolatorThreshold) + -percolatorThreshold $percolator.percolatorThreshold + #end if + </token> + + <xml name="peak_options"> + <section name="peak" expanded="false" title="Peak Options"> + <param argument="-numberOfQuantitativePeaks" type="integer" value="5" min="1" max="100" label="Number of Quantitative Peaks"/> + <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Peaks"/> + <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Ions"/> + <param argument="-minIntensity" type="float" value="-1.0" label="minIntensity"/> + <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" label="Expected Peak Width"/> + <param argument="-filterPeaklists" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Filter Peak Lists"/> + </section> + </xml> + <token name="@PEAK_OPTIONS@"> + #if str($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 + </token> + + <xml name="window_options"> + <section name="window" expanded="false" title="Window Options"> + <param argument="-foffset" type="integer" value="0" label="fragmentOffsetPPM"/> + <param argument="-poffset" type="integer" value="0" label="Precursor Offset PPM" help="-poffset"/> + <param argument="-precursorIsolationMargin" type="integer" value="0" label="precursorIsolationMargin"/> + <param argument="-precursorWindowSize" type="integer" value="-1" label="precursorWindowSize"/> + <param argument="-rtWindowInMin" type="float" value="-1.0" label="rtWindowInMin"/> + <param argument="-scoringBreadthType" type="select" 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> + </section> + </xml> + <token name="@WINDOW_OPTIONS@"> + -foffset $window.foffset + -poffset $window.poffset + -precursorIsolationMargin $window.precursorIsolationMargin + -precursorWindowSize $window.precursorWindowSize + -rtWindowInMin $window.rtWindowInMin + -scoringBreadthType $window.scoringBreadthType + </token> + + <xml name="modification_options"> + <section name="modifications" expanded="false" title="Modification Options"> + <param argument="-fixed" type="select" label="Fixed Modification"> + <option value="C=57.0214635">C=57.0214635</option> + </param> + <!-- + <param argument="-localizationModification" type="select" optional="true" label="localizationModification"> + </param> + --> + <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/> + </section> + </xml> + <token name="@MODIFICATION_OPTIONS@"> + -verifyModificationIons $modifications.verifyModificationIons + </token> + + <xml name="search_options"> + <section name="search" expanded="false" title="Search Options"> + <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="-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"/> + </section> + </xml> + <token name="@SEARCH_OPTIONS@"> + -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 + </token> +minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu + <!-- + +acquisition (default: overlapping dia) + +addDecoysToBackground (default: false) + +alpha (default: 1.8) + +beta (default: 0.4) + +dontRunDecoys (default: false) + +enzyme (default: trypsin) + +filterPeaklists (default: false) + +fixed (default: C=57.0214635) + +foffset (default: 0) + =frag (default: YONLY) + +ftol (default: 10) + +ftolunits (default: ppm) + +maxCharge (default: 3) + +maxLength (default: 100) + +maxMissedCleavage (default: 1) + +minCharge (default: 2) + +minEluteTime (default: 12) + +minIntensity (default: -1.0) + +minLength (default: 5) + +minNumOfQuantitativePeaks (default: 3) + +minQuantitativeIonNumber (default: 3) + +numberOfQuantitativePeaks (default: 5) + -numberOfReportedPeaks (default: 1) + -numberOfThreadsUsed (default: 12) + +percolatorProteinThreshol (default: 0.01) + +percolatorThreshold (default: 0.01) + +percolatorVersionNumber (default: 3) + +poffset (default: 0) + +precursorIsolationMargin (default: 0) + +precursorWindowSize (default: -1) + +ptol (default: 10) + +ptolunits (default: ppm) + -requireVariableMods (default: false) + -variable (default: -) + --> + <xml name="libexport"> + <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files"/> + </xml> +</macros> +<!-- +e w t x l param ++:+:+:+:+ i ++:+:+:+:+ l ++:+:+:+:+ f + ++:+:+:+:+ t +-:+:-:+:- tp +-:+:-:+:+ a + ++:+:+:+:+ o + ++:+:+:+:- acquisition +-:+:-:+:- addDecoysToBackground +-:+:-:+:- alpha +-:+:-:+:- beta +-:-:-:-:+ blib +-:+:-:+:- dontRunDecoys ++:+:+:+:- enzyme ++:-:+:-:- expectedPeakWidth ++:+:+:+:- filterPeaklists ++:+:+:+:+ fixed ++:+:+:+:+ foffset ++:+:+:+:- frag ++:+:+:+:+ ftol ++:+:+:+:+ ftolunits ++:-:+:-:- lftol ++:-:+:-:- lftolunits ++:-:-:-:- libexport ++:-:+:-:+ localizationModification +-:+:-:+:- maxCharge +-:+:-:+:- maxLength +-:+:-:+:- maxMissedCleavage +-:+:-:+:- minCharge +-:+:-:+:- minEluteTime ++:+:+:+:- minIntensity +-:+:-:+:- minLength ++:+:+:+:+ minNumOfQuantitativePeaks ++:+:+:+:+ minQuantitativeIonNumber ++:-:+:-:+ numberOfExtraDecoyLibrariesSearched ++:+:+:+:+ numberOfQuantitativePeaks +-:+:-:+:- numberOfReportedPeaks +-:+:-:+:- numberOfThreadsUsed +-:-:-:-:+ percolatorLocation +-:+:-:+:- percolatorProteinThreshol ++:-:+:-:+ percolatorProteinThreshold ++:+:+:+:+ percolatorThreshold ++:+:+:+:- percolatorVersionNumber +-:-:-:-:+ phospho ++:+:+:+:- poffset ++:+:+:+:- precursorIsolationMargin ++:+:+:+:- precursorWindowSize ++:+:+:+:- ptol ++:+:+:+:- ptolunits +-:+:-:+:- requireVariableMods ++:-:+:-:- rtWindowInMin ++:-:+:-:- scoringBreadthType +-:+:-:+:- variable ++:-:+:-:- verifyModificationIons +-->
--- /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 @@ +<tool id="searchtolib" name="SearchToLib" version="@VERSION@.0"> + <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + @CMD_IMPORTS@ + @LINK_SCAN_INPUTS@ + @LINK_FASTA_INPUT@ + @LINK_TARGET_FASTA@ + for SCAN_FILE in `ls -1 inputs/*`; do + echo "\$SCAN_FILE" && + EncyclopeDIA -Djava.awt.headless=true -Xmx12g $search_app + -i \$SCAN_FILE + @FASTA_INPUT@ + @TARGET_FASTA@ + @COMMON_OPTIONS@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + @SEARCH_OPTIONS@ | tee -a search2lib.log + ; done && + EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport + $search_app + @SCAN_INPUTS@ + @FASTA_INPUT@ + @TARGET_FASTA@ + @COMMON_OPTIONS@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + @SEARCH_OPTIONS@ + -o gxpedia + | tee -a search2lib.log + ]]></command> + <inputs> + <expand macro="scan_inputs"/> + <expand macro="fasta_input"/> + <expand macro="target_fasta"/> + <param name="search_app" type="select" label="Search with"> + <option value="" selected="true">EncyclopeDIA</option> + <option value="-pecan">Pecan</option> + <option value="-xcordia">XCorDIA</option> + </param> + <expand macro="common_options"/> + <expand macro="mass_library_tolerance"/> + <expand macro="percolator_options"/> + <expand macro="peak_options"/> + <expand macro="window_options"/> + <expand macro="modification_options"/> + <expand macro="search_options"/> + <param name="select_outputs" type="select" label="Select outputs" multiple="true"> + <option value="log" selected="true">log</option> + <option value="elib" selected="true">elib</option> + <option value="features" selected="true">concatenated_features.txt</option> + <option value="results" selected="true">concatenated_results.txt</option> + <option value="decoy" selected="true">concatenated_decoy.txt</option> + <option value="peptides" selected="true">peptides.txt</option> + <option value="proteins" selected="true">proteins.txt</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log"> + <filter>'log' in select_outputs</filter> + </data> + <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia"> + <filter>'elib' in select_outputs</filter> + </data> + <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/gxpedia_concatenated_features.txt"> + <filter>'features' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> + </actions> + </data> + <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/gxpedia_concatenated_results.txt"> + <filter>'results' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/gxpedia_concatenated_decoy.txt"> + <filter>'decoy' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="gxpedia.peptides.txt"> + <filter>'peptides' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> + </actions> + </data> + <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="gxpedia.proteins.txt"> + <filter>'proteins' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> + </actions> + </data> + </outputs> + <help><![CDATA[ +SearchToLIB uses EncyclopeDIA, Walnut (Pecan), or XCorDIA to create an DIA Elib for EncyclopeDIA DIA search +Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring. +You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb + +Required Parameters: + -i input .DIA or .MZML file + -f background FASTA file + +Other Parameters: + -t target FASTA file (default: background FASTA file) + -tp true/false target FASTA file contains peptides (default: false) + -o output report file (default: [input file].pecan.txt) + -acquisition (default: overlapping dia) + -addDecoysToBackground (default: false) + -alpha (default: 1.8) + -beta (default: 0.4) + -dontRunDecoys (default: false) + -enzyme (default: trypsin) + -filterPeaklists (default: false) + -fixed (default: C=57.0214635) + -foffset (default: 0) + -frag (default: YONLY) + -ftol (default: 10) + -ftolunits (default: ppm) + -maxCharge (default: 3) + -maxLength (default: 100) + -maxMissedCleavage (default: 1) + -minCharge (default: 2) + -minEluteTime (default: 12) + -minIntensity (default: -1.0) + -minLength (default: 5) + -minNumOfQuantitativePeaks (default: 3) + -minQuantitativeIonNumber (default: 3) + -numberOfQuantitativePeaks (default: 5) + -numberOfReportedPeaks (default: 1) + -numberOfThreadsUsed (default: 12) + -percolatorProteinThreshold (default: 0.01) + -percolatorThreshold (default: 0.01) + -percolatorVersionNumber (default: 3) + -poffset (default: 0) + -precursorIsolationMargin (default: 0) + -precursorWindowSize (default: -1) + -ptol (default: 10) + -ptolunits (default: ppm) + -requireVariableMods (default: false) + -variable (default: -) + + ]]></help> + <expand macro="citations" /> +</tool>
--- /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 @@ +<tool id="walnut" name="Walnut" version="@VERSION@.0"> + <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + @CMD_IMPORTS@ + @LINK_SCAN_INPUT@ + @LINK_FASTA_INPUT@ + @LINK_TARGET_FASTA@ + EncyclopeDIA -Djava.awt.headless=true -Xmx12g -walnut + @SCAN_INPUT@ + @FASTA_INPUT@ + @TARGET_FASTA@ + @COMMON_OPTIONS@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + @SEARCH_OPTIONS@ + -o gxpedia + ]]></command> + <inputs> + <expand macro="scan_input"/> + <expand macro="fasta_input"/> + <expand macro="target_fasta"/> + <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"/> + <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> + <option value="features" selected="true">features.txt</option> + <option value="pecan" selected="true">pecan.txt</option> + <option value="pecan_decoy" selected="true">pecan.decoy.txt</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> + <filter>'log' in select_outputs</filter> + </data> + <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib"> + <filter>'elib' in select_outputs</filter> + </data> + <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt"> + <filter>'features' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> + </actions> + </data> + <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt"> + <filter>'pecan' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt"> + <filter>'pecan_decoy' in select_outputs</filter> + <actions> + <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> + </actions> + </data> + </outputs> + <help><![CDATA[ +Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring. +You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb + +Required Parameters: + -i input .DIA or .MZML file + -f background FASTA file + +Other Parameters: + -t target FASTA file (default: background FASTA file) + -tp true/false target FASTA file contains peptides (default: false) + -o output report file (default: [input file].pecan.txt) + -acquisition (default: overlapping dia) + -addDecoysToBackground (default: false) + -alpha (default: 1.8) + -beta (default: 0.4) + -dontRunDecoys (default: false) + -enzyme (default: trypsin) + -filterPeaklists (default: false) + -fixed (default: C=57.0214635) + -foffset (default: 0) + -frag (default: YONLY) + -ftol (default: 10) + -ftolunits (default: ppm) + -maxCharge (default: 3) + -maxLength (default: 100) + -maxMissedCleavage (default: 1) + -minCharge (default: 2) + -minEluteTime (default: 12) + -minIntensity (default: -1.0) + -minLength (default: 5) + -minNumOfQuantitativePeaks (default: 3) + -minQuantitativeIonNumber (default: 3) + -numberOfQuantitativePeaks (default: 5) + -numberOfReportedPeaks (default: 1) + -numberOfThreadsUsed (default: 12) + -percolatorProteinThreshold (default: 0.01) + -percolatorThreshold (default: 0.01) + -percolatorVersionNumber (default: 3) + -poffset (default: 0) + -precursorIsolationMargin (default: 0) + -precursorWindowSize (default: -1) + -ptol (default: 10) + -ptolunits (default: ppm) + -requireVariableMods (default: false) + -variable (default: -) + + ]]></help> + <expand macro="citations" /> +</tool>