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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<tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @SEARCH2LIB_CMDS@ ]]></command> <inputs> <expand macro="scan_inputs"/> <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> <expand macro="fasta_input"/> <expand macro="target_fasta"/> <expand macro="options_section"/> <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> <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="false">concatenated_features.txt</option> <option value="results" selected="true">concatenated_results.txt</option> <option value="decoy" selected="false">concatenated_decoy.txt</option> <option value="rt_plots" selected="false">Retention Time Plots</option> <option value="rt_tables" selected="false">Retention Time Tables</option> <option value="peptides" selected="true">peptides.txt (requires align between files)</option> <option value="proteins" selected="true">proteins.txt (requires align between files)</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} ${on_string} elib" from_work_dir="chromatogram_library.elib"> <filter>'elib' in select_outputs</filter> </data> <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt"> <filter>'features' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> </actions> </data> <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt"> <filter>'results' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt"> <filter>'decoy' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots"> <filter>library and 'rt_plots' in select_outputs</filter> <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" directory="inputs"/> </collection> <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> <filter>library and 'rt_tables' in select_outputs</filter> <discover_datasets pattern="(?P<designation>.+\.mzML\..+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> </collection> <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> <filter>a and 'peptides' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> </actions> </data> <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt"> <filter>a and 'proteins' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> </actions> </data> </outputs> <tests> <test> <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/> <param name="library" ftype="elib" value="BCS_hela.elib"/> <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/> <output name="results" ftype="tabular"> <assert_contents> <has_text text="GIEQAVQSHAVAEEEAR"/> </assert_contents> </output> <output name="peptides" ftype="tabular"> <assert_contents> <has_text text="AYPLADAHLTK"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **EncyclopeDIA Quantify** @ENCYCLOPEDIA_WIKI@ EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. **Inputs** - Spectrum files in mzML format - A chromatogram library that can be generated by SearchToLib - A protein data base in fasta format @MSCONVERT_HELP@ **Outputs** - A log file - A Chromatogram Library (.elib) - The identified features in tabular format Feature values of scans that are used by percolator to determine matches. - The identified Peptide Spectral Match results in tabular format Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds - The identified peptides in tabular format Per peptide: the normalized intensity for each scan file. Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ... - The identified proteins in tabular format Per protein: the normalized intensity for each scan file. Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ... **Typical DIA SearchToLib Workflow** Two sets of Mass Spec MS/MS DIA data are collected for the experiment. In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments. 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library. If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file. Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring. * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage. 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results. .. image:: SearchToLib_Workflow.png :width: 810 :height: 580 .. _Prosit: https://www.proteomicsdb.org/prosit ]]></help> <expand macro="citations" /> </tool>