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comparison encyclopedia_quantify.xml @ 0:d3a6bc607825 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
author jjohnson
date Tue, 30 Jun 2020 11:34:57 -0400
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children acf6acfc8632
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-1:000000000000 0:d3a6bc607825
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>