Mercurial > repos > jjohnson > encyclopedia_quantify

comparison encyclopedia_quantify.xml @ 5:30f6b9c88ceb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
comparison
equal deleted inserted replaced
4:bd937e4efa04 5:30f6b9c88ceb
44 <expand macro="options_section"/> 44 <expand macro="options_section"/>
45 <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"/> 45 <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"/>
46 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> 46 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
47 <option value="log" selected="true">log</option> 47 <option value="log" selected="true">log</option>
48 <option value="elib" selected="true">elib</option> 48 <option value="elib" selected="true">elib</option>
49 <option value="features" selected="true">concatenated_features.txt</option> 49 <option value="features" selected="false">concatenated_features.txt</option>
50 <option value="results" selected="true">concatenated_results.txt</option> 50 <option value="results" selected="true">concatenated_results.txt</option>
51 <option value="decoy" selected="false">concatenated_decoy.txt</option> 51 <option value="decoy" selected="false">concatenated_decoy.txt</option>
52 <!--
53 <option value="rt_plots" selected="false">Retention Time Plots</option> 52 <option value="rt_plots" selected="false">Retention Time Plots</option>
54 <option value="rt_tables" selected="false">Retention Time Tables</option> 53 <option value="rt_tables" selected="false">Retention Time Tables</option>
55 -->
56 <option value="peptides" selected="true">peptides.txt (requires align between files)</option> 54 <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
57 <option value="proteins" selected="true">proteins.txt (requires align between files)</option> 55 <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
58 </param> 56 </param>
59 </inputs> 57 </inputs>
60 <outputs> 58 <outputs>
80 <filter>'decoy' in select_outputs</filter> 78 <filter>'decoy' in select_outputs</filter>
81 <actions> 79 <actions>
82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 80 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
83 </actions> 81 </actions>
84 </data> 82 </data>
85 <!--
86 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots"> 83 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
87 <filter>l and 'rt_plots' in select_outputs</filter> 84 <filter>library and 'rt_plots' in select_outputs</filter>
88 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/> 85 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
89 </collection> 86 </collection>
90 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> 87 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
91 <filter>l and 'rt_tables' in select_outputs</filter> 88 <filter>library and 'rt_tables' in select_outputs</filter>
92 <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> 89 <discover_datasets pattern="(?P&lt;designation&gt;.+\.mzML\..+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
93 </collection> 90 </collection>
94 -->
95 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> 91 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
96 <filter>a and 'peptides' in select_outputs</filter> 92 <filter>a and 'peptides' in select_outputs</filter>
97 <actions> 93 <actions>
98 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> 94 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
99 </actions> 95 </actions>
128 124
129 @ENCYCLOPEDIA_WIKI@ 125 @ENCYCLOPEDIA_WIKI@
130 126
131 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. 127 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results.
132 128
129
130 **Inputs**
131
132 - Spectrum files in mzML format
133 - A chromatogram library that can be generated by SearchToLib
134 - A protein data base in fasta format
135
133 @MSCONVERT_HELP@ 136 @MSCONVERT_HELP@
137
138 **Outputs**
139
140 - A log file
141 - A Chromatogram Library (.elib)
142 - The identified features in tabular format
143 Feature values of scans that are used by percolator to determine matches.
144 - The identified Peptide Spectral Match results in tabular format
145 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
146 - The identified peptides in tabular format
147 Per peptide: the normalized intensity for each scan file.
148 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
149 - The identified proteins in tabular format
150 Per protein: the normalized intensity for each scan file.
151 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
152
134 153
135 **Typical DIA SearchToLib Workflow** 154 **Typical DIA SearchToLib Workflow**
136 155
137 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. 156 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.
138 157