Mercurial > repos > jjohnson > encyclopedia_searchtolib
changeset 6:7efddaece152 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
author | jjohnson |
---|---|
date | Fri, 21 Aug 2020 16:13:47 -0400 |
parents | b9c8e02d1405 |
children | 29309591ca3e |
files | encyclopedia_searchtolib.xml macros.xml |
diffstat | 2 files changed, 30 insertions(+), 17 deletions(-) [+] |
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--- a/encyclopedia_searchtolib.xml Wed Aug 19 08:40:05 2020 -0400 +++ b/encyclopedia_searchtolib.xml Fri Aug 21 16:13:47 2020 -0400 @@ -55,12 +55,10 @@ <option value="features" selected="false">concatenated_features.txt</option> <option value="results" selected="false">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="rt_plots" selected="false">Retention Time Plots (requires library)</option> + <option value="rt_tables" selected="false">Retention Time Tables (requires library)</option> <option value="peptides" selected="false">peptides.txt (requires align between files)</option> <option value="proteins" selected="false">proteins.txt (requires align between files)</option> - --> </param> </inputs> <outputs> @@ -88,18 +86,14 @@ <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} - ${on_string}: Retention Time Plots"> - <filter>l and 'rt_plots' in select_outputs</filter> + <filter>library and 'rt_plots' in select_outputs</filter> <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" directory="inputs"/> </collection> <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> - <filter>l and 'rt_tables' in select_outputs</filter> - <discover_datasets pattern="(?P<designation>.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> + <filter>library and 'rt_tables' in select_outputs</filter> + <discover_datasets pattern="(?P<designation>.+\.mzML\..*\.rt_fit\.txt)" ext="tabular" directory="inputs"/> </collection> - --> - - <!-- <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> <filter>a and 'peptides' in select_outputs</filter> <actions> @@ -112,7 +106,6 @@ <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> </actions> </data> - --> </outputs> <tests> <test> @@ -128,17 +121,37 @@ </test> </tests> <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 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. + + +**Inputs** -SearchToLIB can also quantify peptides from the chromatogram library. + - Spectrum files in mzML format + - A protein data base in fasta format + - An optional DDA Spectral library (.dlib) that can be generated by Prosit + - *SearchToLIB uses Enclopedia if the Prosit dlib is provided, otherwise it uses Walnut with just a fasta.* @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 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.
--- a/macros.xml Wed Aug 19 08:40:05 2020 -0400 +++ b/macros.xml Fri Aug 21 16:13:47 2020 -0400 @@ -128,7 +128,7 @@ <token name="@LINK_LIB_INPUT@"><![CDATA[ #if $library #set $l_name = $ln_name($library) - cp '$library' $l_name && + cp '$library' '$l_name' && #else #set $l_name = None #end if @@ -494,7 +494,7 @@ </token> <token name="@MSCONVERT_HELP@"><![CDATA[ - The MSConvert command can be used to deconvolute DIA raw files. You need to use these options + The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options: ::