Mercurial > repos > jjohnson > encyclopedia_quantify
comparison encyclopedia_quantify.xml @ 0:d3a6bc607825 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
author | jjohnson |
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date | Tue, 30 Jun 2020 11:34:57 -0400 |
parents | |
children | acf6acfc8632 |
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-1:000000000000 | 0:d3a6bc607825 |
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1 <tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@VERSION@.0"> | |
2 <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 @CMD_IMPORTS@ | |
9 @LINK_SCAN_INPUTS@ | |
10 @LINK_FASTA_INPUT@ | |
11 @LINK_TARGET_FASTA@ | |
12 @LINK_LIB_INPUT@ | |
13 for SCAN_FILE in `ls -1 inputs/*`; do | |
14 echo "\$SCAN_FILE" && | |
15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g | |
16 -i \$SCAN_FILE | |
17 @FASTA_INPUT@ | |
18 @TARGET_FASTA@ | |
19 @LIB_INPUT@ | |
20 @COMMON_OPTIONS@ | |
21 @MASS_LIBRARY_TOLERANCE@ | |
22 @PERCOLATOR_OPTIONS@ | |
23 @PEAK_OPTIONS@ | |
24 @WINDOW_OPTIONS@ | |
25 @MODIFICATION_OPTIONS@ | |
26 @SEARCH_OPTIONS@ | tee -a search2lib.log | |
27 ; done && | |
28 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport | |
29 @SCAN_INPUTS@ | |
30 @FASTA_INPUT@ | |
31 @TARGET_FASTA@ | |
32 @LIB_INPUT@ | |
33 -a $a | |
34 -o chromatogram_library.elib | |
35 | tee -a search2lib.log | |
36 ]]></command> | |
37 <inputs> | |
38 <expand macro="scan_inputs"/> | |
39 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/> | |
40 <expand macro="fasta_input"/> | |
41 <expand macro="target_fasta"/> | |
42 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/> | |
43 <expand macro="common_options"/> | |
44 <expand macro="mass_library_tolerance"/> | |
45 <expand macro="percolator_options"/> | |
46 <expand macro="peak_options"/> | |
47 <expand macro="window_options"/> | |
48 <expand macro="modification_options"/> | |
49 <expand macro="search_options"/> | |
50 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> | |
51 <option value="log" selected="true">log</option> | |
52 <option value="elib" selected="true">elib</option> | |
53 <option value="features" selected="true">concatenated_features.txt</option> | |
54 <option value="results" selected="true">concatenated_results.txt</option> | |
55 <option value="decoy" selected="false">concatenated_decoy.txt</option> | |
56 <option value="peptides" selected="true">peptides.txt (requires align between files)</option> | |
57 <option value="proteins" selected="true">proteins.txt (requires align between files)</option> | |
58 </param> | |
59 </inputs> | |
60 <outputs> | |
61 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log"> | |
62 <filter>'log' in select_outputs</filter> | |
63 </data> | |
64 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib"> | |
65 <filter>'elib' in select_outputs</filter> | |
66 </data> | |
67 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt"> | |
68 <filter>'features' in select_outputs</filter> | |
69 <actions> | |
70 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" /> | |
71 </actions> | |
72 </data> | |
73 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt"> | |
74 <filter>'results' in select_outputs</filter> | |
75 <actions> | |
76 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> | |
77 </actions> | |
78 </data> | |
79 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt"> | |
80 <filter>'decoy' in select_outputs</filter> | |
81 <actions> | |
82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> | |
83 </actions> | |
84 </data> | |
85 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> | |
86 <filter>a and 'peptides' in select_outputs</filter> | |
87 <actions> | |
88 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> | |
89 </actions> | |
90 </data> | |
91 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> | |
92 <filter>a and 'proteins' in select_outputs</filter> | |
93 <actions> | |
94 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" /> | |
95 </actions> | |
96 </data> | |
97 </outputs> | |
98 <help><![CDATA[ | |
99 | |
100 **EncyclopeDIA Quantify** | |
101 | |
102 @ENCYCLOPEDIA_WIKI@ | |
103 | |
104 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results. | |
105 | |
106 @MSCONVERT_HELP@ | |
107 | |
108 **Typical DIA SearchToLib Workflow** | |
109 | |
110 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. | |
111 | |
112 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library. | |
113 If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file. | |
114 Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring. | |
115 | |
116 | |
117 * 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. | |
118 | |
119 | |
120 2. EncyclopeDIA Quantify 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. | |
121 | |
122 .. image:: SearchToLib_Workflow.png | |
123 :height: 439 | |
124 :width: 768 | |
125 | |
126 .. _Prosit: https://www.proteomicsdb.org/prosit | |
127 | |
128 ]]></help> | |
129 <expand macro="citations" /> | |
130 </tool> |