Mercurial > repos > jjohnson > encyclopedia_walnut
changeset 3:e37e3c4a87a9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"
| author | jjohnson |
|---|---|
| date | Thu, 02 Jul 2020 11:10:14 -0400 |
| parents | 114b44e35d30 |
| children | 2f36eba0b877 |
| files | encyclopedia_searchtolib.xml.bak macros.xml |
| diffstat | 2 files changed, 1 insertions(+), 138 deletions(-) [+] |
line wrap: on
line diff
--- a/encyclopedia_searchtolib.xml.bak Wed Jul 01 11:24:59 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -<tool id="encyclopedia_searchtolib" name="SearchToLib" version="@VERSION@.0"> - <description>Build a Chromatogram Library or quantify 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[ - @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 -Xmx20g - #if not $l - -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 && - EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport - #if not $l - -pecan - #end if - @SCAN_INPUTS@ - @FASTA_INPUT@ - @TARGET_FASTA@ - @LIB_INPUT@ - -a $a - -o chromatogram_library.elib - | tee -a search2lib.log - ]]></command> - <inputs> - <expand macro="scan_inputs"/> - <expand macro="lib_input" optional="true" libhelp="Use a Chromatogram elib for quantification, or a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/> - <expand macro="fasta_input"/> - <expand macro="target_fasta"/> - <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> - <expand macro="common_options"/> - <expand macro="mass_library_tolerance"/> - <expand macro="percolator_options"/> - <expand macro="peak_options"/> - <expand macro="window_options"/> - <expand macro="modification_options"/> - <expand macro="search_options"/> - <param name="select_outputs" type="select" label="Select outputs" multiple="true"> - <option value="log" selected="true">log</option> - <option value="elib" selected="true">elib</option> - <option value="features" selected="true">concatenated_features.txt</option> - <option value="results" selected="true">concatenated_results.txt</option> - <option value="decoy" selected="false">concatenated_decoy.txt</option> - <option value="peptides" selected="true">peptides.txt (requires match between runs)</option> - <option value="proteins" selected="true">proteins.txt (requires match between runs)</option> - </param> - </inputs> - <outputs> - <data name="log" format="txt" label="${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} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt"> - <filter>'decoy' in select_outputs</filter> - <actions> - <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> - </actions> - </data> - <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> - <filter>a and 'peptides' in select_outputs</filter> - <actions> - <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> - </actions> - </data> - <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> - <filter>a and 'proteins' in select_outputs</filter> - <actions> - <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> - </actions> - </data> - </outputs> - <help><![CDATA[ - -**SearchToLIB** - -@ENCYCLOPEDIA_WIKI@ - -SearchToLIB uses the EncyclopeDIA algorithm, or the Walnut (Pecan) algorithm to search Data-Independent Acquisition (DIA) MS/MS spectrum files and creates a DIA elib chromatogram library for EncyclopeDIA DIA quantitation search. - -SearchToLIB can also quantify peptides from the chromatogram library. - -@MSCONVERT_HELP@ - -**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. SearchToLib 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 - :height: 439 - :width: 768 - -.. _Prosit: https://www.proteomicsdb.org/prosit - - ]]></help> - <expand macro="citations" /> -</tool>