Mercurial > repos > jjohnson > encyclopedia_encyclopedia
view encyclopedia_encyclopedia.xml @ 0:36f9910c85c4 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author | jjohnson |
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date | Fri, 19 Jun 2020 10:13:10 -0400 |
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children | b4f1a49ff3b5 |
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<tool id="encyclopedia_encyclopedia" name="EncyclopeDIA" version="@VERSION@.0"> <description>Library Searching 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_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" token_optional="false" token_help="Chromatogram elib from SearchToLib"/> <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>