Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 6:7efddaece152 draft

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"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
comparison
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5:b9c8e02d1405 6:7efddaece152
53 <option value="log" selected="true">log</option> 53 <option value="log" selected="true">log</option>
54 <option value="elib" selected="true">elib</option> 54 <option value="elib" selected="true">elib</option>
55 <option value="features" selected="false">concatenated_features.txt</option> 55 <option value="features" selected="false">concatenated_features.txt</option>
56 <option value="results" selected="false">concatenated_results.txt</option> 56 <option value="results" selected="false">concatenated_results.txt</option>
57 <option value="decoy" selected="false">concatenated_decoy.txt</option> 57 <option value="decoy" selected="false">concatenated_decoy.txt</option>
58 <!-- 58 <option value="rt_plots" selected="false">Retention Time Plots (requires library)</option>
59 <option value="rt_plots" selected="false">Retention Time Plots</option> 59 <option value="rt_tables" selected="false">Retention Time Tables (requires library)</option>
60 <option value="rt_tables" selected="false">Retention Time Tables</option>
61 <option value="peptides" selected="false">peptides.txt (requires align between files)</option> 60 <option value="peptides" selected="false">peptides.txt (requires align between files)</option>
62 <option value="proteins" selected="false">proteins.txt (requires align between files)</option> 61 <option value="proteins" selected="false">proteins.txt (requires align between files)</option>
63 -->
64 </param> 62 </param>
65 </inputs> 63 </inputs>
66 <outputs> 64 <outputs>
67 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log"> 65 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
68 <filter>'log' in select_outputs</filter> 66 <filter>'log' in select_outputs</filter>
86 <filter>'decoy' in select_outputs</filter> 84 <filter>'decoy' in select_outputs</filter>
87 <actions> 85 <actions>
88 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 86 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
89 </actions> 87 </actions>
90 </data> 88 </data>
91 <!--
92 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots"> 89 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
93 <filter>l and 'rt_plots' in select_outputs</filter> 90 <filter>library and 'rt_plots' in select_outputs</filter>
94 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/> 91 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
95 </collection> 92 </collection>
96 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> 93 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
97 <filter>l and 'rt_tables' in select_outputs</filter> 94 <filter>library and 'rt_tables' in select_outputs</filter>
98 <discover_datasets pattern="(?P&lt;designation&gt;.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> 95 <discover_datasets pattern="(?P&lt;designation&gt;.+\.mzML\..*\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
99 </collection> 96 </collection>
100 -->
101
102 <!--
103 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> 97 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
104 <filter>a and 'peptides' in select_outputs</filter> 98 <filter>a and 'peptides' in select_outputs</filter>
105 <actions> 99 <actions>
106 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> 100 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
107 </actions> 101 </actions>
110 <filter>a and 'proteins' in select_outputs</filter> 104 <filter>a and 'proteins' in select_outputs</filter>
111 <actions> 105 <actions>
112 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> 106 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
113 </actions> 107 </actions>
114 </data> 108 </data>
115 -->
116 </outputs> 109 </outputs>
117 <tests> 110 <tests>
118 <test> 111 <test>
119 <param name="scan_inputs" ftype="mzml" value="BCS_hela_narrow_3_1.mzML,BCS_hela_narrow_3_2.mzML"/> 112 <param name="scan_inputs" ftype="mzml" value="BCS_hela_narrow_3_1.mzML,BCS_hela_narrow_3_2.mzML"/>
120 <param name="library" ftype="dlib" value="small_pan_human_library.dlib"/> 113 <param name="library" ftype="dlib" value="small_pan_human_library.dlib"/>
126 </assert_contents> 119 </assert_contents>
127 </output> 120 </output>
128 </test> 121 </test>
129 </tests> 122 </tests>
130 <help><![CDATA[ 123 <help><![CDATA[
131
132 **SearchToLIB** 124 **SearchToLIB**
133 125
134 @ENCYCLOPEDIA_WIKI@ 126 @ENCYCLOPEDIA_WIKI@
135 127
136 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. 128 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.
137 129
138 SearchToLIB can also quantify peptides from the chromatogram library. 130
131 **Inputs**
132
133 - Spectrum files in mzML format
134 - A protein data base in fasta format
135 - An optional DDA Spectral library (.dlib) that can be generated by Prosit
136 - *SearchToLIB uses Enclopedia if the Prosit dlib is provided, otherwise it uses Walnut with just a fasta.*
139 137
140 @MSCONVERT_HELP@ 138 @MSCONVERT_HELP@
139
140 **Outputs**
141
142 - A log file
143 - A Chromatogram Library (.elib)
144 - The identified features in tabular format
145 Feature values of scans that are used by percolator to determine matches.
146 - The identified Peptide Spectral Match results in tabular format
147 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
148 - The identified peptides in tabular format
149 Per peptide: the normalized intensity for each scan file.
150 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
151 - The identified proteins in tabular format
152 Per protein: the normalized intensity for each scan file.
153 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
141 154
142 **Typical DIA Workflow** 155 **Typical DIA Workflow**
143 156
144 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. 157 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.
145 158