Mercurial > repos > jjohnson > encyclopedia_quantify
diff encyclopedia_quantify.xml @ 5:30f6b9c88ceb draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
author | jjohnson |
---|---|
date | Fri, 21 Aug 2020 16:11:54 -0400 |
parents | bd937e4efa04 |
children | 5a5da160f667 |
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--- a/encyclopedia_quantify.xml Wed Aug 19 08:38:25 2020 -0400 +++ b/encyclopedia_quantify.xml Fri Aug 21 16:11:54 2020 -0400 @@ -46,13 +46,11 @@ <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="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> @@ -82,16 +80,14 @@ <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> @@ -130,8 +126,31 @@ 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.