Mercurial > repos > jjohnson > encyclopedia_encyclopedia
diff 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 |
|---|---|
| date | Fri, 19 Jun 2020 10:13:10 -0400 |
| parents | |
| children | b4f1a49ff3b5 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_encyclopedia.xml Fri Jun 19 10:13:10 2020 -0400 @@ -0,0 +1,140 @@ +<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>